I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 11 05:27:44 -12 2022 I: pbuilder-time-stamp: 1662917264 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [hhsuite_3.0~beta3+dfsg-3.dsc] I: copying [./hhsuite_3.0~beta3+dfsg.orig.tar.xz] I: copying [./hhsuite_3.0~beta3+dfsg-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 15 06:07:29 2019 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hhsuite_3.0~beta3+dfsg-3.dsc dpkg-source: info: extracting hhsuite in hhsuite-3.0~beta3+dfsg dpkg-source: info: unpacking hhsuite_3.0~beta3+dfsg.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.0~beta3+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying add_Makefile_in_data.patch dpkg-source: info: applying disable-ffindex-build.patch dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying build-own-manual-PDF.patch dpkg-source: info: applying set-default-HHLIB-dir.patch dpkg-source: info: applying disable-AVX-SSE.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/57341/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b6a03a9362714585a6f52ae28c07179e' 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='57341' 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/tmp.UkQopsrZCQ/pbuilderrc_AQnB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UkQopsrZCQ/b1 --logfile b1/build.log hhsuite_3.0~beta3+dfsg-3.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 9 02:47 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/57341/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 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 (>= 11~), libffindex0-dev (>= 0.9.9.8), cmake, texlive-latex-base, texlive-latex-recommended, imagemagick, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libffindex0-dev (>= 0.9.9.8); however: Package libffindex0-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake 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-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} bsdmainutils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcroco3{a} libcups2{a} libcupsimage2{a} libcurl4{a} libdbus-1-3{a} libde265-0{a} libelf1{a} libexpat1{a} libffindex0{a} libffindex0-dev{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libheif1{a} libice6{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libncurses6{a} libnghttp2-14{a} libnuma1{a} libopenjp2-7{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpotrace0{a} libprocps7{a} libpsl5{a} libptexenc1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libtexluajit2{a} libtiff5{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libwebpmux3{a} libwoff1{a} libx11-6{a} libx11-data{a} libx265-165{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} libxt6{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} po-debconf{a} poppler-data{a} procps{a} sensible-utils{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-latex-base{a} texlive-latex-recommended{a} ucf{a} x11-common{a} xdg-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus fonts-droid-fallback ghostscript gsfonts krb5-locales libarchive-cpio-perl libcupsfilters1 libfile-mimeinfo-perl libglib2.0-data libgpm2 libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lmodern lynx netpbm psmisc publicsuffix shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 144 newly installed, 0 to remove and 0 not upgraded. Need to get 107 MB of archives. After unpacking 368 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libfftw3-double3 amd64 3.3.8-2 [733 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libde265-0 amd64 1.0.3-1+b1 [240 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libx265-165 amd64 2.9-4 [1041 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libheif1 amd64 1.3.2-2~deb10u1 [127 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 liblqr-1-0 amd64 0.4.2-2.1 [29.1 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libopenjp2-7 amd64 2.3.0-2+deb10u2 [158 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 imagemagick-6-common all 8:6.9.10.23+dfsg-2.1+deb10u1 [200 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libmagickcore-6.q16-6 amd64 8:6.9.10.23+dfsg-2.1+deb10u1 [1786 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libmagickwand-6.q16-6 amd64 8:6.9.10.23+dfsg-2.1+deb10u1 [446 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 poppler-data all 0.4.9-2 [1473 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 tex-common all 6.11 [53.1 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 fonts-lmodern all 2.004.5-6 [4539 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 imagemagick-6.q16 amd64 8:6.9.10.23+dfsg-2.1+deb10u1 [580 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 imagemagick amd64 8:6.9.10.23+dfsg-2.1+deb10u1 [156 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 libbrotli1 amd64 1.0.7-2+deb10u1 [269 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libcupsimage2 amd64 2.2.10-6+deb10u4 [133 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libffindex0 amd64 0.9.9.9-2 [18.0 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libffindex0-dev amd64 0.9.9.9-2 [19.1 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libgs9-common all 9.27~dfsg-2+deb10u4 [5136 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libijs-0.35 amd64 0.35-14 [18.3 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 libjbig2dec0 amd64 0.16-1 [62.0 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libgs9 amd64 9.27~dfsg-2+deb10u4 [2195 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libharfbuzz-icu0 amd64 2.3.1-1 [834 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libkpathsea6 amd64 2018.20181218.49446-1 [167 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libpotrace0 amd64 1.15-1 [26.3 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libptexenc1 amd64 2018.20181218.49446-1 [61.0 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libsynctex2 amd64 2018.20181218.49446-1 [80.5 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libteckit0 amd64 2.5.8+ds2-5 [318 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 libtexlua52 amd64 2018.20181218.49446-1 [112 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libtexlua53 amd64 2018.20181218.49446-1 [126 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libtexluajit2 amd64 2018.20181218.49446-1 [256 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libwoff1 amd64 1.0.2-1 [43.2 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 libxxhash0 amd64 0.6.5-2 [7156 B] Get: 138 http://deb.debian.org/debian buster/main amd64 libzzip-0-13 amd64 0.13.62-3.2 [55.4 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 texlive-binaries amd64 2018.20181218.49446-1 [11.3 MB] Get: 141 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 142 http://deb.debian.org/debian buster/main amd64 texlive-base all 2018.20190227-2 [19.7 MB] Get: 143 http://deb.debian.org/debian buster/main amd64 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 144 http://deb.debian.org/debian buster/main amd64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Fetched 107 MB in 3s (39.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../006-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../007-libfftw3-double3_3.3.8-2_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.8-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../008-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../009-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../010-libfreetype6_2.9.1-3+deb10u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../011-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../012-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../013-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../014-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../015-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package libde265-0:amd64. Preparing to unpack .../016-libde265-0_1.0.3-1+b1_amd64.deb ... Unpacking libde265-0:amd64 (1.0.3-1+b1) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../017-libnuma1_2.0.12-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1) ... Selecting previously unselected package libx265-165:amd64. Preparing to unpack .../018-libx265-165_2.9-4_amd64.deb ... Unpacking libx265-165:amd64 (2.9-4) ... Selecting previously unselected package libheif1:amd64. Preparing to unpack .../019-libheif1_1.3.2-2~deb10u1_amd64.deb ... Unpacking libheif1:amd64 (1.3.2-2~deb10u1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../020-libjbig0_2.1-3.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../021-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../022-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../023-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package liblqr-1-0:amd64. Preparing to unpack .../024-liblqr-1-0_0.4.2-2.1_amd64.deb ... Unpacking liblqr-1-0:amd64 (0.4.2-2.1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../025-libltdl7_2.4.6-9_amd64.deb ... Unpacking libltdl7:amd64 (2.4.6-9) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../026-libopenjp2-7_2.3.0-2+deb10u2_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.3.0-2+deb10u2) ... Selecting previously unselected package libwebp6:amd64. Preparing to unpack .../027-libwebp6_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libtiff5:amd64. Preparing to unpack .../028-libtiff5_4.1.0+git191117-2~deb10u2_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u2) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../029-libwebpmux3_0.6.1-2+deb10u1_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../030-libxau6_1%3a1.0.8-1+b2_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../031-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../032-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../033-libx11-data_2%3a1.6.7-1+deb10u2_all.deb ... Unpacking libx11-data (2:1.6.7-1+deb10u2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../034-libx11-6_2%3a1.6.7-1+deb10u2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../035-libxext6_2%3a1.3.3-1+b2_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.3-1+b2) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../036-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../037-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../038-imagemagick-6-common_8%3a6.9.10.23+dfsg-2.1+deb10u1_all.deb ... Unpacking imagemagick-6-common (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickcore-6.q16-6:amd64. Preparing to unpack .../039-libmagickcore-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_amd64.deb ... Unpacking libmagickcore-6.q16-6:amd64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickwand-6.q16-6:amd64. Preparing to unpack .../040-libmagickwand-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_amd64.deb ... Unpacking libmagickwand-6.q16-6:amd64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../041-poppler-data_0.4.9-2_all.deb ... Unpacking poppler-data (0.4.9-2) ... Selecting previously unselected package tex-common. Preparing to unpack .../042-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../043-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:amd64. Preparing to unpack .../044-libprocps7_2%3a3.3.15-2_amd64.deb ... Unpacking libprocps7:amd64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../045-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../046-procps_2%3a3.3.15-2_amd64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../047-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../048-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../049-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../050-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../051-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../052-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../053-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. 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I: Building the package I: Running cd /build/hhsuite-3.0~beta3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.0~beta3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --builddirectory=mybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/hhsuite-3.0~beta3+dfsg' dh_auto_clean rm -f hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg' dh_autoreconf_clean -O--builddirectory=mybuild dh_clean -O--builddirectory=mybuild debian/rules build dh build --builddirectory=mybuild dh_update_autotools_config -O--builddirectory=mybuild dh_autoreconf -O--builddirectory=mybuild dh_auto_configure -O--builddirectory=mybuild cd mybuild && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 8.3.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU -- Processor is x86_64 -- Performing Test HAVE_MM_MALLOC -- Performing Test HAVE_MM_MALLOC - Success -- Performing Test HAVE_POSIX_MEMALIGN -- Performing Test HAVE_POSIX_MEMALIGN - Success -- Performing Test HAVE_AVX2_EXTENSIONS -- Performing Test HAVE_AVX2_EXTENSIONS - Success -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_SSE4_2_EXTENSIONS -- Performing Test HAVE_SSE4_2_EXTENSIONS - Success -- Performing Test HAVE_SSE4_1_EXTENSIONS -- Performing Test HAVE_SSE4_1_EXTENSIONS - Success -- Performing Test HAVE_SSSE3_EXTENSIONS -- Performing Test HAVE_SSSE3_EXTENSIONS - Success -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_SSE2_EXTENSIONS -- Performing Test HAVE_SSE2_EXTENSIONS - Success -- Performing Test HAVE_SSE_EXTENSIONS -- Performing Test HAVE_SSE_EXTENSIONS - Success -- Found SSE4.2 extensions, using flags: -msse4.2 -mfpmath=sse -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Found LATEX: /usr/bin/latex -- Found UnixCommands: /bin/bash -- I could not find the ps2pdf command. -- I could not find the pdftops command. -- I could not find the latex2html command. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hhsuite-3.0~beta3+dfsg/mybuild debian/rules override_dh_auto_build make[1]: Entering directory '/build/hhsuite-3.0~beta3+dfsg' dh_auto_build -- NO_PNG=1 cd mybuild && make -j16 "INSTALL=install --strip-program=true" NO_PNG=1 make[2]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/cmake -S"/build/hhsuite-3.0~beta3+dfsg" -B"/build/hhsuite-3.0~beta3+dfsg/mybuild" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles" "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles/progress.marks" make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake" --color= Scanning dependencies of target A3M_COMPRESS_OBJECT make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/doc" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc/CMakeFiles/pdf.dir/DependInfo.cmake" --color= Scanning dependencies of target CS_OBJECTS make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build Scanning dependencies of target hhviterbialgorithm_with_celloff Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 1%] Building CXX object src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build Scanning dependencies of target pdf cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 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[11] [12]In file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:22: /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void end_of_options() const throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const std::string& long_opt) throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] template inline T getopt(char short_opt) throw(GetOptEx) { ^~~~~ [13] LaTeX Warning: Citation `Gonzalez:2010' on page 14 undefined on input line 612. LaTeX Warning: Reference `MAC' on page 14 undefined on input line 612. [14] Underfull \hbox (badness 10000) in paragraph at lines 648--649 [15] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10.95 $ python3 cif2fasta.py -i -o pdb100.fas -c -p pdb_filter.dat[] LaTeX Warning: Reference `building_dbs' on page 16 undefined on input line 721. [16] LaTeX Warning: Reference `building_dbs' on page 17 undefined on input line 738. Overfull \hbox (18.0163pt too wide) in paragraph at lines 738--739 []\OT1/cmr/m/n/10.95 which both were cre-ated by [][]\OT1/cmtt/m/n/10.95 cif2fa sta.py[]\OT1/cmr/m/n/10.95 , and the clus-ter as-sign-ments from MM-Seqs ([][]\ OT1/cmtt/m/n/10.95 pdb70_clu.tsv[]\OT1/cmr/m/n/10.95 ) Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [17]/build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:115:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const _Option& opt) throw (GetOptEx) { ^~~~~ Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] LaTeX Warning: Citation `Todd:2001' on page 18 undefined on input line 801. LaTeX Warning: Citation `Pawlowski:2000' on page 18 undefined on input line 801 . LaTeX Warning: Citation `Rychlewski:1998' on page 18 undefined on input line 80 1. LaTeX Warning: Citation `Kinch:2002' on page 18 undefined on input line 801. LaTeX Warning: Citation `Soding:2006a' on page 18 undefined on input line 801. LaTeX Warning: Citation `Alva:2010' on page 18 undefined on input line 801. [18] LaTeX Warning: Citation `Chothia:1986' on page 19 undefined on input line 804. LaTeX Warning: Citation `Todd:2001' on page 19 undefined on input line 804. LaTeX Warning: Citation `Alva:2010' on page 19 undefined on input line 804. LaTeX Warning: Citation `Remmert:2010' on page 19 undefined on input line 804. [19] LaTeX Warning: Citation `Soding:2006b' on page 20 undefined on input line 835. LaTeX Warning: Citation `Mariani:2011' on page 20 undefined on input line 839. LaTeX Warning: Citation `Battey:2007' on page 20 undefined on input line 839. 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Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Pr_1 81 GAFLIRESESA-PGDFSLSVKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Consensus 81 ~~~~~~~~~~~-~~~~~~s~~~~~~~~~~~i~~~~ ~~~~~~~~~~f~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 [] \OT1/cmtt/m/n/10.95 |.+++|.+... ++.+.+ +..++.++|+++.... .+.|+.+...|.++..++.++...+....................[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T Consensus 81 G~flvR~s~~~~~~~~~l-v~~~~~v~h~~i~~~~ ~g~~~~~~~~f~sl~~Lv~~y~~~~~~~~~~~~l~~~~~~~~~~~ 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T 1gri_A 81 GAFLIRESESAPGDFSLS-VKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_dssp TCEEEEECSSSTTCEEEE-EEETTEEEEEEEEECS SSCEESSSCEESSHHHHHHHHHHSCSSSSTTCCCCBCCCCCCCCC[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] [25] LaTeX Warning: Reference `msa_hhblits' on page 26 undefined on input line 998. [26] [27] [28] [29] [30] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [31] LaTeX Warning: Reference `msa_hhblits' on page 32 undefined on input line 1435. Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits [32] [33] LaTeX Warning: Reference `transformation' on page 34 undefined on input line 15 19. LaTeX Warning: Reference `transformation' on page 34 undefined on input line 15 19. LaTeX Warning: Reference `transformation' on page 34 undefined on input line 15 19. [34] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [35] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] [36] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [37] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [38] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [40] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [41] [42] [43] LaTeX Warning: Citation `Sali:1993' on page 44 undefined on input line 2101. LaTeX Warning: Citation `Sali:1993' on page 44 undefined on input line 2138. [44] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] LaTeX Warning: Reference `building_dbs' on page 46 undefined on input line 2242 . LaTeX Warning: Reference `building_dbs' on page 46 undefined on input line 2265 . [46] [47] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . LaTeX Warning: Citation `Remmert:2011' on page 48 undefined on input line 2386. [48] [49] [50] LaTeX Warning: Citation `Farrar:2007' on page 51 undefined on input line 2548. Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [51] No file hhsuite-userguide.bbl. [52] (./hhsuite-userguide.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (52 pages, 379486 bytes). Transcript written on hhsuite-userguide.log. cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/bibtex hhsuite-userguide [ 30%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalign.cpp" This is BibTeX, Version 0.99d (TeX Live 2019/dev/Debian) The top-level auxiliary file: hhsuite-userguide.aux The style file: unsrt.bst Database file #1: hhsuite-userguide.bib cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex In file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.h:29, from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.cc:21: /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void end_of_options() const throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const std::string& long_opt) throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] template inline T getopt(char short_opt) throw(GetOptEx) { ^~~~~ This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' entering extended mode (./hhsuite-userguide.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo[ 31%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o ))cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhitlist.cpp" (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/cite/cite.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/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[ 31%] Built target A3M_COMPRESS_OBJECT )))make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[20]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake" --color= LaTeX Warning: Citation `Soding:2006b' on page 21 undefined on input line 835. LaTeX Warning: Citation `Mariani:2011' on page 21 undefined on input line 839. LaTeX Warning: Citation `Battey:2007' on page 21 undefined on input line 839. LaTeX Warning: Citation `Durbin:2008' on page 21 undefined on input line 849. LaTeX Warning: Citation `Biegert:2008' on page 21 undefined on input line 849. LaTeX Warning: Citation `Soding:2005b' on page 21 undefined on input line 861. LaTeX Warning: Citation `Hildebrand:2009' on page 21 undefined on input line 86 1. 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[25make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake" --color= ] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Pr_1 81 GAFLIRESESA-PGDFSLSVKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Consensus 81 ~~~~~~~~~~~-~~~~~~s~~~~~~~~~~~i~~~~ ~~~~~~~~~~f~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 [] \OT1/cmtt/m/n/10.95 |.+++|.+... ++.+.+ +..++.++|+++.... .+.|+.+...|.++..++.++...+....................[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T Consensus 81 G~flvR~s~~~~~~~~~l-v~~~~~v~h~~i~~~~ ~g~~~~~~~~f~sl~~Lv~~y~~~~~~~~~~~~l~~~~~~~~~~~ 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T 1gri_A 81 GAFLIRESESAPGDFSLS-VKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_dssp TCEEEEECSSSTTCEEEE-EEETTEEEEEEEEECS SSCEESSSCEESSHHHHHHHHHHSCSSSSTTCCCCBCCCCCCCCC[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] [26] [27]Scanning dependencies of target a3m_reduce make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [28]make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build [29]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [30] [31Scanning dependencies of target a3m_extract ] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [32make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' ]make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits [33]make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [34] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [36[ 39%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o ] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] [37] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [38cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_reduce.cpp" ] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [39][ 40%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/a3m_extract.cpp" Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [40] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [41] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [42] [43][ 42%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhutil.cpp" [44] LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2101. LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2138. [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [46] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [47] [48] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . LaTeX Warning: Citation `Remmert:2011' on page 49 undefined on input line 2386. [49] [50] [51] LaTeX Warning: Citation `Farrar:2007' on page 52 undefined on input line 2548. Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [52] (./hhsuite-userguide.bbl [53] [54]) [55] (./hhsuite-userguide.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (55 pages, 393238 bytes). Transcript written on hhsuite-userguide.log. cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /build/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./hhsuite-userguide.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/cite/cite.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/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/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[6] Underfull \hbox (badness 10000) in paragraph at lines 235--236 Overfull \hbox (30.66537pt too wide) in paragraph at lines 240--240 []\OT1/cmtt/m/n/10.95 $ wget https://github.com/soedinglab/hh-suite/releases/.. ./hhsuite-3.0-beta.1-Linux.rpm[] Underfull \hbox (badness 10000) in paragraph at lines 243--245 [7]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_filter -lffindex Overfull \hbox (82.40356pt too wide) in paragraph at lines 307--307 []\OT1/cmtt/m/n/10.95 $ wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/data bases/hhsuite_dbs/uniprot20_2015_06.tgz[] [8] [9] [10] [11 <./hhblits-hhsearch.png[ 46%] Linking CXX executable ../bin/a3m_database_reduce cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_reduce -lffindex [ 46%] Built target CS_OBJECTS [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp" [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhforwardalgorithm.cpp" make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 49%] Built target a3m_database_filter [ 50%] Linking CXX executable ../bin/a3m_reduce cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhmm.cpp" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_reduce -lffindex >] [12] [13] [14][ 53%] Linking CXX executable ../bin/a3m_database_extract cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 [15] Underfull \hbox (badness 10000) in paragraph at lines 648--649 [16]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10.95 $ python3 cif2fasta.py -i -o pdb100.fas -c -p pdb_filter.dat[] [17] Overfull \hbox (18.0163pt too wide) in paragraph at lines 738--739 []\OT1/cmr/m/n/10.95 which both were cre-ated by [][]\OT1/cmtt/m/n/10.95 cif2fa sta.py[]\OT1/cmr/m/n/10.95 , and the clus-ter as-sign-ments from MM-Seqs ([][]\ OT1/cmtt/m/n/10.95 pdb70_clu.tsv[]\OT1/cmr/m/n/10.95 ) Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [18]/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_extract -lffindex Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] [19] [20][ 53%] Built target a3m_database_reduce [21] [22] [23] [24] [25] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Pr_1 81 GAFLIRESESA-PGDFSLSVKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Consensus 81 ~~~~~~~~~~~-~~~~~~s~~~~~~~~~~~i~~~~ ~~~~~~~~~~f~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 [] \OT1/cmtt/m/n/10.95 |.+++|.+... ++.+.+ +..++.++|+++.... .+.|+.+...|.++..++.++...+....................[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T Consensus 81 G~flvR~s~~~~~~~~~l-v~~~~~v~h~~i~~~~ ~g~~~~~~~~f~sl~~Lv~~y~~~~~~~~~~~~l~~~~~~~~~~~ 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T 1gri_A 81 GAFLIRESESAPGDFSLS-VKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_dssp TCEEEEECSSSTTCEEEE-EEETTEEEEEEEEECS SSCEESSSCEESSHHHHHHHHHHSCSSSSTTCCCCBCCCCCCCCC[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] [26][ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhposteriordecoderrunner.cpp" [27] [28] [29] [30] [31] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [32] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits [33] [34] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [36] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] [37] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [38] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [40] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [41]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [42] [43]make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [44] [45][ 55%] Built target a3m_database_extract Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [46][ 55%] Built target a3m_reduce Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [47] [48][ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . [49] [50] [51][ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [52]cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhfullalignment.cpp" (./hhsuite-userguide.bbl[ 59%] Linking CXX executable ../bin/a3m_extract [53] [54]) [55] (./hhsuite-userguide.auxcd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 ) ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (55 pages, 394812 bytes). Transcript written on hhsuite-userguide.log. make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 59%] Built target pdf [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhmmsimd.cpp" make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 60%] Built target a3m_extract [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhposteriormatrix.cpp" [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbi.cpp" [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhbacktracemac.cpp" [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhmacalgorithm.cpp" [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhprefilter.cpp" [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbimatrix.cpp" [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhbackwardalgorithm.cpp" [ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhdatabase.cpp" [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhhalfalignment.cpp" [ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhviterbirunner.cpp" [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhfunc.cpp" /build/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp:1797:24: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] sprintf(details, "The alingment %s does not contain any sequences.", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/bits/locale_classes.h:40, from /usr/include/c++/8/bits/ios_base.h:41, from /usr/include/c++/8/ios:42, from /usr/include/c++/8/ostream:38, from /usr/include/c++/8/iostream:39, from /build/hhsuite-3.0~beta3+dfsg/src/hhalignment.h:3, from /build/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 47 and 4142 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 76%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake" --color= make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake" --color= Scanning dependencies of target hhblits make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake" --color= Scanning dependencies of target cstranslate make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake" --color= make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Scanning dependencies of target hhblits_omp make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Scanning dependencies of target hhconsensus make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Scanning dependencies of target hhsearch make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build Scanning dependencies of target hhalign make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Scanning dependencies of target hhmake [ 78%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhblits_app.cpp" make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 79%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o Scanning dependencies of target hhfilter cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c "/build/hhsuite-3.0~beta3+dfsg/src/cs/cstranslate_app.cc" make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build [ 81%] Building CXX object src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhblits_omp.cpp" make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 82%] Building CXX object src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhconsensus.cpp" [ 84%] Building CXX object src/CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o [ 85%] Building CXX object src/CMakeFiles/hhalign.dir/hhalign_app.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhalign.dir/hhalign_app.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhalign_app.cpp" cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhsearch_app.cpp" [ 86%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhmake.cpp" [ 88%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/build/hhsuite-3.0~beta3+dfsg/src" -I"/build/hhsuite-3.0~beta3+dfsg/src/cs" -I"/build/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c "/build/hhsuite-3.0~beta3+dfsg/src/hhfilter.cpp" In file included from /build/hhsuite-3.0~beta3+dfsg/src/cs/application.h:29, from /build/hhsuite-3.0~beta3+dfsg/src/cs/cstranslate_app.h:22, from /build/hhsuite-3.0~beta3+dfsg/src/cs/cstranslate_app.cc:20: /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void end_of_options() const throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const std::string& long_opt) throw(GetOptEx) { ^~~~~ /build/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] template inline T getopt(char short_opt) throw(GetOptEx) { ^~~~~ [ 89%] Linking CXX executable ../bin/hhblits cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhblits -lffindex [ 91%] Linking CXX executable ../bin/hhalign cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign.dir/hhalign_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhalign -lffindex make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 91%] Built target hhblits make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 91%] Built target hhalign [ 92%] Linking CXX executable ../bin/hhsearch cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhsearch -lffindex [ 94%] Linking CXX executable ../bin/hhmake cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhmake -lffindex [ 95%] Linking CXX executable ../bin/hhfilter /build/hhsuite-3.0~beta3+dfsg/src/hhblits_omp.cpp: In function 'int main(int, char**)': /build/hhsuite-3.0~beta3+dfsg/src/hhblits_omp.cpp:32:46: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /build/hhsuite-3.0~beta3+dfsg/src/hhblits_omp.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhfilter -lffindex make[4]: 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CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o 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make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 98%] Built target hhblits_omp [100%] Linking CXX executable ../bin/cstranslate cd "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/cstranslate -lffindex make[4]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/cmake -E cmake_progress_start "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles" 0 make[2]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[1]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg' dh_auto_test -O--builddirectory=mybuild cd mybuild && make -j16 test ARGS\+=-j16 make[1]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Running tests... 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"/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make[3]: 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"/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build make[3]: Entering 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'/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_filter.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build [ 10%] Built target a3m_database_filter make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_reduce.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_extract.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_reduce.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_extract.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 13%] Built target a3m_database_reduce [ 15%] Built target a3m_database_extract [ 18%] Built target a3m_reduce [ 21%] Built target a3m_extract make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/CS_OBJECTS.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 31%] Built target CS_OBJECTS make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 33%] Built target hhviterbialgorithm_with_celloff [ 34%] Built target hhviterbialgorithm_and_ss [ 36%] Built target hhviterbialgorithm_with_celloff_and_ss make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/HH_OBJECTS.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 76%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' cd "/build/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/hhsuite-3.0~beta3+dfsg" "/build/hhsuite-3.0~beta3+dfsg/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src" "/build/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhfilter.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhmake.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhblits.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhconsensus.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/cstranslate.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhblits_omp.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhalign.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhsearch.dir/build'. make[3]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' [ 79%] Built target hhfilter [ 82%] Built target hhblits [ 85%] Built target hhmake [ 88%] Built target cstranslate [ 91%] Built target hhblits_omp [ 94%] Built target hhconsensus [ 97%] Built target hhalign [100%] Built target hhsearch make[2]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/cmake -E cmake_progress_start "/build/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles" 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/./LICENSE -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/./README -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhblits_omp -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhblits -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhmake -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhfilter -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhsearch -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhalign -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/hhconsensus -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/a3m_extract -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/a3m_database_extract -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/a3m_database_filter -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/bin/cstranslate -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/context_data.crf -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/context_data.lib -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/cs219.lib -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/do_not_delete -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/do_not_delete.phr -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/do_not_delete.pin -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/data/do_not_delete.psq -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/Align.pm -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/addss.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/mergeali.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/multithread.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/reformat.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/splitfasta.pl -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/check_a3m.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/ffindex.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/a3m.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/pdbfilter.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/cif2fasta.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/hhmakemodel.py -- Installing: /build/hhsuite-3.0~beta3+dfsg/debian/tmp/usr/scripts/hh_reader.py make[1]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg/mybuild' dh_install -O--builddirectory=mybuild dh_installdocs -O--builddirectory=mybuild dh_installchangelogs -O--builddirectory=mybuild dh_installexamples -O--builddirectory=mybuild debian/rules override_dh_installman make[1]: Entering directory '/build/hhsuite-3.0~beta3+dfsg' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhblits_omp" 'debian/tmp/usr/bin/hhblits_omp' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits_omp.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhconsensus" 'debian/tmp/usr/bin/hhconsensus' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhconsensus.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhfilter" 'debian/tmp/usr/bin/hhfilter' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhfilter.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhmake" 'debian/tmp/usr/bin/hhmake' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhmake.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta3+dfsg -n "$n_hhsearch" 'debian/tmp/usr/bin/hhsearch' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhsearch.1' dh_installman make[1]: Leaving directory '/build/hhsuite-3.0~beta3+dfsg' dh_installinit -O--builddirectory=mybuild dh_perl -O--builddirectory=mybuild dh_link -O--builddirectory=mybuild dh_strip_nondeterminism -O--builddirectory=mybuild dh_compress -O--builddirectory=mybuild dh_fixperms -O--builddirectory=mybuild dh_missing -O--builddirectory=mybuild dh_strip -O--builddirectory=mybuild dh_makeshlibs -O--builddirectory=mybuild dh_shlibdeps -O--builddirectory=mybuild dh_installdeb -O--builddirectory=mybuild dh_gencontrol -O--builddirectory=mybuild dpkg-gencontrol: warning: Depends field of package hhsuite-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package hhsuite: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package hhsuite: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--builddirectory=mybuild dh_builddeb -O--builddirectory=mybuild dpkg-deb: building package 'hhsuite' in '../hhsuite_3.0~beta3+dfsg-3_amd64.deb'. dpkg-deb: building package 'hhsuite-doc' in '../hhsuite-doc_3.0~beta3+dfsg-3_all.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.0~beta3+dfsg-3_all.deb'. dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.0~beta3+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hhsuite_3.0~beta3+dfsg-3_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) 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/57341 and its subdirectories I: Current time: Sun Sep 11 05:30:44 -12 2022 I: pbuilder-time-stamp: 1662917444