sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | mummer 3.23+dfsg-8 (amd64) Tue, 04 Jun 2024 17:05:44 +0000 | +==============================================================================+ Package: mummer Version: 3.23+dfsg-8 Source Version: 3.23+dfsg-8 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-aa96851c-a0d3-4741-8bad-9b10dd2e18c9' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mummer_3.23+dfsg-8 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mummer_3.23+dfsg-8 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/mummer-263isP/resolver-miqVLo' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 http://localhost:3142/debian unstable InRelease [198 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:3 http://localhost:3142/debian sid InRelease [198 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB] Get:6 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB] Fetched 659 kB in 2s (288 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 login passwd util-linux 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3414 kB of archives. After this operation, 57.3 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.1-8 [104 kB] Get:2 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.1-8 [137 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.1-8 [34.7 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.1-8 [166 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.1-8 [197 kB] Get:7 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.1-8 [1210 kB] Get:8 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3414 kB in 0s (101 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/mummer_3.23+dfsg-8.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/mummer-263isP/mummer-3.23+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/mummer-263isP' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [691 B] Get:5 copy:/<>/apt_archive ./ Packages [723 B] Fetched 2023 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcairo2 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libice6 libicu72 libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libsm6 libsynctex2 libteckit0 libtexlua53-5 libtool libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db po-debconf sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff low-memory-monitor libmpfi-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex texlive-latex-recommended-doc texlive-luatex texlive-pstricks Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl lmodern dvisvgm tex-gyre tipa libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcairo2 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libice6 libicu72 libkpathsea6 libmagic-mgc libmagic1t64 libmpfi0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16t64 libpotrace0 libptexenc1 libsm6 libsynctex2 libteckit0 libtexlua53-5 libtool libuchardet0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils t1utils tex-common texlive-base texlive-binaries texlive-fonts-recommended texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 81.7 MB of archives. After this operation, 251 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-8 [96.0 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:12 http://localhost:3142/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:13 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:15 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:20 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:23 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:24 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:25 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:28 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:29 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:30 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:33 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:34 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:35 http://localhost:3142/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:36 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:37 http://localhost:3142/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:58 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-2 [156 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-3 [35.1 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:64 http://localhost:3142/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-2 [48.5 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-2 [62.2 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-2 [113 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get:76 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:77 http://localhost:3142/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get:78 http://localhost:3142/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-2 [8438 kB] Get:79 http://localhost:3142/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:80 http://localhost:3142/debian unstable/main amd64 texlive-base all 2024.20240401-2 [22.7 MB] Get:81 http://localhost:3142/debian unstable/main amd64 texlive-fonts-recommended all 2024.20240401-2 [4990 kB] Get:82 http://localhost:3142/debian unstable/main amd64 texlive-latex-base all 2024.20240401-2 [1258 kB] Get:83 http://localhost:3142/debian unstable/main amd64 texlive-latex-recommended all 2024.20240401-2 [8847 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 81.7 MB in 0s (167 MB/s) Selecting previously unselected package sensible-utils. 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Preparing to unpack .../82-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libxau6:amd64 (1:1.0.9-1+b1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.34-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-2) ... No schema files found: doing nothing. Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up autopoint (0.21-14) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-2) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:amd64 (2024.20240313.70630+ds-2) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up debhelper (13.15.3) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up texlive-binaries (2024.20240313.70630+ds-2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240401-2) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up texlive-latex-base (2024.20240401-2) ... Setting up texlive-latex-recommended (2024.20240401-2) ... Setting up texlive-fonts-recommended (2024.20240401-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-8 bsdutils_1:2.40.1-8 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-8 libbrotli1_1.1.0-2+b3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcairo2_1.18.0-3+b1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libexpat1_2.6.2-1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libfontconfig1_2.15.0-1.1 libfreetype6_2.13.2+dfsg-1+b4 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libglib2.0-0t64_2.80.2-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libgraphite2-3_1.3.14-2 libharfbuzz0b_8.3.0-2+b1 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libice6_2:1.0.10-1+b1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libkpathsea6_2024.20240313.70630+ds-2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-8 libmpc3_1.3.1-1+b2 libmpfi0_1.5.4+ds-3 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpaper-utils_1.1.29+b1 libpaper1_1.1.29+b1 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libpixman-1-0_0.42.2-1+b1 libpng16-16t64_1.6.43-5 libpotrace0_1.16-2+b1 libptexenc1_2024.20240313.70630+ds-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsm6_2:1.2.3-1+b1 libsmartcols1_2.40.1-8 libsqlite3-0_3.46.0-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsynctex2_2024.20240313.70630+ds-2 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libteckit0_2.5.12+ds1-1 libtexlua53-5_2024.20240313.70630+ds-2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-8 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxaw7_2:1.0.14-1+b2 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b1 libxi6_2:1.8.1-1 libxml2_2.12.7+dfsg-3 libxmu6_2:1.1.3-3+b2 libxpm4_1:3.5.17-1+b1 libxrender1_1:0.9.10-1.1+b1 libxt6t64_1:1.2.1-1.2 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 libzzip-0-13t64_0.13.72+dfsg.1-1.2+b1 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-5 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 t1utils_1.41-4 tar_1.35+dfsg-3 tex-common_6.18 texlive-base_2024.20240401-2 texlive-binaries_2024.20240313.70630+ds-2 texlive-fonts-recommended_2024.20240401-2 texlive-latex-base_2024.20240401-2 texlive-latex-recommended_2024.20240401-2 ucf_3.0043+nmu1 usr-is-merged_39 util-linux_2.40.1-8 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mummer Binary: mummer, mummer-doc Architecture: any all Version: 3.23+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy Homepage: https://mummer.sourceforge.net/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/mummer Vcs-Git: https://salsa.debian.org/med-team/mummer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended Package-List: mummer deb science optional arch=any mummer-doc deb doc optional arch=all Checksums-Sha1: 0dc589e7ceeb59d222ec21decf225ba193527330 1112616 mummer_3.23+dfsg.orig.tar.xz 01b4363663073e877e4562a7426f715d13a2eab8 416352 mummer_3.23+dfsg-8.debian.tar.xz Checksums-Sha256: 1ef5eb11b22ff39d930ea9168ed6852a28be2c21e29ac791c4edcc86eca7d805 1112616 mummer_3.23+dfsg.orig.tar.xz 864d465c88d62db2150fe616ce20e3e640263e39b3d9eb85a3cef053d5ccec49 416352 mummer_3.23+dfsg-8.debian.tar.xz Files: 64c8ac0f462885f9978b9e49accbc71f 1112616 mummer_3.23+dfsg.orig.tar.xz 16ae45f82d20b64c4eb583a8aef7275f 416352 mummer_3.23+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOMhm8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHIZA//eUDhdfkDfyZByP7wPkFgHPcx/EEPDTiY YU0jpxYvcxPwibV3gKrlK9pdycowU2xhuLgfsQ3+Iq019Dz+cL//EPGDCNAh8U7p qnXX4cnV1afFAyB5mE2Z0GDYDt9OeyV/SUTE+6qIDa7ri0PvWl8k+UYwJgZ4Qu30 N5pATtkhm0WcRSuVIBBeieFlvPT4iXVP1OrKbACY7VWoPd4xhVXVLGIIuyg6eid9 C71WxafyBNuV/klWk1f4WmcTNpM/+OuWtcfZrfiU3zc6fTX43k93MS/BZxQmsiRS b39Dw5KDii3JDPwsQDMSpvmmhW18lJkGlIRO9Pe/3zAYzyl6sB36xqFpWvszd5AY 9j7Doxc47OGoB5h9nD1VpFIXz4B2/icc8rEUjvorLMfYedfGCMB021E9YbqToGUk +l3ziWgK+Tpk+boF1jWSOqw8mjoRPoOydlSE0wyC9GiMQ02W3EuWnr1NlfWP00aW wf00Akp6s55wtU9/KWHwCR4tLrCvxaBmMUKUTY4WIUvRgSDdM18sS8RdwXDAZUBG HCMC7jqsy9adgwSuDoy49MEpkScZ3DlL0cRdlX8WP/p4WpG9NKmte6GA+8GF60RG CEqfz52Nho4jDsK6bqMLrbM/GZ/YG+QoHfDn1HTpSdaVSGvuE+S3MjcJt4bWW/tK hg8rQICZlQ4= =+dC6 -----END PGP SIGNATURE----- gpgv: Signature made Sun Dec 4 11:37:19 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mummer_3.23+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting mummer in /<> dpkg-source: info: unpacking mummer_3.23+dfsg.orig.tar.xz dpkg-source: info: unpacking mummer_3.23+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_install_dirs.patch dpkg-source: info: applying 02at_docs_web.diff dpkg-source: info: applying enable_building_with_tetex.patch dpkg-source: info: applying fix_sf_privacy_breach_issue.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying addition_from_mugsy.patch dpkg-source: info: applying 0009-improve-performance-of-delta2maf.patch dpkg-source: info: applying mummerplot.patch dpkg-source: info: applying remove-csh-dependency.patch dpkg-source: info: applying remove-csh-from-doc.patch dpkg-source: info: applying reproducible-build.patch dpkg-source: info: applying gnuplot.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mummer_3.23+dfsg-8 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mummer_3.23+dfsg-8 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-aa96851c-a0d3-4741-8bad-9b10dd2e18c9 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package mummer dpkg-buildpackage: info: source version 3.23+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/<>' rm -f *~ core* cd /<>/src/kurtz; make clean make[2]: Entering directory '/<>/src/kurtz' rm -f *~ cd libbasedir; make clean make[3]: Entering directory '/<>/src/kurtz/libbasedir' rm -f *.splint rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log *~ make[3]: Leaving directory '/<>/src/kurtz/libbasedir' cd streesrc; make clean make[3]: Entering directory '/<>/src/kurtz/streesrc' rm -f *.splint rm -f *.[aox] *~ make[3]: Leaving directory '/<>/src/kurtz/streesrc' cd mm3src; make clean make[3]: Entering directory '/<>/src/kurtz/mm3src' rm -f *.splint rm -f *.[ox] shit[123] *~ cd /<>; rm -f maxmat3.x maxmat3.dbg.x mummer make[3]: Leaving directory '/<>/src/kurtz/mm3src' make[2]: Leaving directory '/<>/src/kurtz' cd /<>/src/tigr; make clean make[2]: Entering directory '/<>/src/tigr' rm -f *.o *~ cd /<>; rm -f annotate combineMUMs delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns show-coords show-tiling show-snps show-diff delta2blocks delta2maf cd /<>/aux_bin; rm -f annotate combineMUMs delta-filter gaps mgaps postnuc postpro prenuc prepro repeat-match show-aligns show-coords show-tiling show-snps show-diff delta2blocks delta2maf make[2]: Leaving directory '/<>/src/tigr' cd /<>/scripts; make clean make[2]: Entering directory '/<>/scripts' rm -f *~ cd /<>; rm -f exact-tandems mapview mummerplot nucmer promer run-mummer1 run-mummer3 nucmer2xfig dnadiff make[2]: Leaving directory '/<>/scripts' cd /<>/docs; make clean make[2]: Entering directory '/<>/docs' rm -f *.dvi *.aux *.log *.out *~ maxmat3man.pdf make[2]: Leaving directory '/<>/docs' make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building mummer using existing ./mummer_3.23+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building mummer in mummer_3.23+dfsg-8.debian.tar.xz dpkg-source: info: building mummer in mummer_3.23+dfsg-8.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' [ -d /<>/debian/tmp/usr/bin ] || mkdir -p /<>/debian/tmp/usr/bin [ -d /<>/debian/tmp/usr/lib/mummer ] || mkdir -p /<>/debian/tmp/usr/lib/mummer dh_auto_build -- BIN_DIR=/<>/debian/tmp/usr/bin AUX_BIN_DIR=/<>/debian/tmp/usr/lib/mummer \ FINAL_BIN_DIR=/usr/bin FINAL_AUX_BIN_DIR=/usr/lib/mummer \ FINAL_SCRIPT_DIR=/usr/share/perl5/ \ CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j2 "INSTALL=install --strip-program=true" BIN_DIR=/<>/mummer-3.23\+dfsg/debian/tmp/usr/bin AUX_BIN_DIR=/<>/mummer-3.23\+dfsg/debian/tmp/usr/lib/mummer FINAL_BIN_DIR=/usr/bin FINAL_AUX_BIN_DIR=/usr/lib/mummer FINAL_SCRIPT_DIR=/usr/share/perl5/ "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc" "CXXFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' cd /<>/src/kurtz; make mummer cd /<>/src/tigr; make CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc" CXXFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection" LDFLAGS="-Wl,-z,relro -Wl,-z,now" all make[3]: Entering directory '/<>/src/kurtz' cd libbasedir; make libbase.a make[3]: Entering directory '/<>/src/tigr' /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 tigrinc.cc -c -o tigrinc.o make[4]: Entering directory '/<>/src/kurtz/libbasedir' /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cleanMUMcand.o cleanMUMcand.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o clock.o clock.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mapfile.o mapfile.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multiseq.o multiseq.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o procopt.o procopt.c tigrinc.cc: In function ‘int Read_String(FILE*, char*&, long int&, char*, int)’: tigrinc.cc:335:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fgets (Line, MAX_LINE, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ tigrinc.cc: In function ‘int Read_File(FILE*, long int&, std::map, char*>&, int)’: tigrinc.cc:452:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 452 | fgets (Line, MAX_LINE, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o safescpy.o safescpy.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seterror.o seterror.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o space.o space.c ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o safescpy.o seterror.o space.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libbase.a a - cleanMUMcand.o a - clock.o a - mapfile.o a - multiseq.o a - procopt.o a - safescpy.o a - seterror.o a - space.o make[4]: Leaving directory '/<>/src/kurtz/libbasedir' cd streesrc; make libstree.a make[4]: Entering directory '/<>/src/kurtz/streesrc' /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o construct.o construct.c /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 delta.cc -c -o delta.o /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o access.o access.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o scanpref.o scanpref.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o linkloc.o linkloc.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o depthtab.o depthtab.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ex2leav.o ex2leav.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dfs.o dfs.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o overmax.o overmax.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o oversucc.o oversucc.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addleafcount.o addleafcount.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -DSTREEHUGE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o iterator.o iterator.c ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libstree.a a - construct.o a - access.o a - scanpref.o a - linkloc.o a - depthtab.o a - ex2leav.o a - dfs.o a - overmax.o a - oversucc.o a - addleafcount.o a - iterator.o make[4]: Leaving directory '/<>/src/kurtz/streesrc' cd mm3src; make mummer make[4]: Entering directory '/<>/src/kurtz/mm3src' /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o maxmat3.o maxmat3.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o maxmatopt.o maxmatopt.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o maxmatinp.o maxmatinp.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o findmumcand.o findmumcand.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o findmaxmat.o findmaxmat.c /usr/bin/gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSTREEHUGE -I/<>/src/kurtz/libbasedir -I/<>/src/kurtz/streesrc -I../libbasedir -I../streesrc -Wdate-time -D_FORTIFY_SOURCE=2 -c -o procmaxmat.o procmaxmat.c /usr/bin/gcc -Wl,-z,relro -Wl,-z,now maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ -o /<>/debian/tmp/usr/bin/mummer; chmod 755 /<>/debian/tmp/usr/bin/mummer make[4]: Leaving directory '/<>/src/kurtz/mm3src' make[3]: Leaving directory '/<>/src/kurtz' cd /<>/scripts; make all make[3]: Entering directory '/<>/scripts' cp -a ../debian/sh-replacement-scripts/exact-tandems /<>/debian/tmp/usr/bin chmod 755 /<>/debian/tmp/usr/bin/exact-tandems /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/usr/share/perl5/?g' \ mapview.pl > /<>/debian/tmp/usr/bin/mapview chmod 755 /<>/debian/tmp/usr/bin/mapview /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/usr/share/perl5/?g' \ -e 's?__BIN_DIR?/usr/bin?g' \ mummerplot.pl > /<>/debian/tmp/usr/bin/mummerplot chmod 755 /<>/debian/tmp/usr/bin/mummerplot /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/usr/share/perl5/?g' \ -e 's?__AUX_BIN_DIR?/usr/lib/mummer?g' \ -e 's?__BIN_DIR?/usr/bin?g' \ nucmer.pl > /<>/debian/tmp/usr/bin/nucmer chmod 755 /<>/debian/tmp/usr/bin/nucmer /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/usr/share/perl5/?g' \ -e 's?__AUX_BIN_DIR?/usr/lib/mummer?g' \ -e 's?__BIN_DIR?/usr/bin?g' \ promer.pl > /<>/debian/tmp/usr/bin/promer chmod 755 /<>/debian/tmp/usr/bin/promer cp -a ../debian/sh-replacement-scripts/run-mummer1 /<>/debian/tmp/usr/bin chmod 755 /<>/debian/tmp/usr/bin/run-mummer1 cp -a ../debian/sh-replacement-scripts/run-mummer3 /<>/debian/tmp/usr/bin chmod 755 /<>/debian/tmp/usr/bin/run-mummer3 /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ nucmer2xfig.pl > /<>/debian/tmp/usr/bin/nucmer2xfig chmod 755 /<>/debian/tmp/usr/bin/nucmer2xfig /usr/bin/sed -e 's?__PERL_PATH?/usr/bin/perl?g' \ -e 's?__SCRIPT_DIR?/usr/share/perl5/?g' \ -e 's?__BIN_DIR?/usr/bin?g' \ dnadiff.pl > /<>/debian/tmp/usr/bin/dnadiff chmod 755 /<>/debian/tmp/usr/bin/dnadiff make[3]: Leaving directory '/<>/scripts' /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now gaps.cc tigrinc.o -o /<>/debian/tmp/usr/bin/gaps; chmod 755 /<>/debian/tmp/usr/bin/gaps /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now mgaps.cc tigrinc.o -o /<>/debian/tmp/usr/bin/mgaps; chmod 755 /<>/debian/tmp/usr/bin/mgaps /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 sw_align.cc -c -o sw_align.o mgaps.cc: In function ‘int Process_Cluster(Match_t*, int, char*)’: mgaps.cc:533:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 533 | label = "#\n"; | ^~~~~ mgaps.cc: In function ‘void Process_Matches(Match_t*, int, char*)’: mgaps.cc:620:19: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 620 | label = "#\n"; | ^~~~~ /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 translate.cc -c -o translate.o /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now prenuc.cc tigrinc.o -o /<>/debian/tmp/usr/lib/mummer/prenuc; chmod 755 /<>/debian/tmp/usr/lib/mummer/prenuc /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now prepro.cc tigrinc.o translate.o -o /<>/debian/tmp/usr/lib/mummer/prepro; chmod 755 /<>/debian/tmp/usr/lib/mummer/prepro /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now repeat-match.cc tigrinc.o -o /<>/debian/tmp/usr/bin/repeat-match; chmod 755 /<>/debian/tmp/usr/bin/repeat-match /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now show-aligns.cc tigrinc.o translate.o delta.o -o /<>/debian/tmp/usr/bin/show-aligns; chmod 755 /<>/debian/tmp/usr/bin/show-aligns /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now show-coords.cc tigrinc.o delta.o -o /<>/debian/tmp/usr/bin/show-coords; chmod 755 /<>/debian/tmp/usr/bin/show-coords show-coords.cc: In function ‘void printBtab(std::vector)’: show-coords.cc:799:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 799 | type = "NUCMER"; | ^~~~~~~~ show-coords.cc:801:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 801 | type = "PROMER"; | ^~~~~~~~ show-coords.cc:803:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 803 | type = "NULL"; | ^~~~~~ /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now show-tiling.cc tigrinc.o delta.o -o /<>/debian/tmp/usr/bin/show-tiling; chmod 755 /<>/debian/tmp/usr/bin/show-tiling /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now show-snps.cc tigrinc.o translate.o delta.o -o /<>/debian/tmp/usr/bin/show-snps; chmod 755 /<>/debian/tmp/usr/bin/show-snps /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now show-diff.cc tigrinc.o delta.o -o /<>/debian/tmp/usr/bin/show-diff; chmod 755 /<>/debian/tmp/usr/bin/show-diff /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now delta2blocks.cc tigrinc.o translate.o delta.o -o /<>/debian/tmp/usr/bin/delta2blocks; chmod 755 /<>/debian/tmp/usr/bin/delta2blocks /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now delta2maf.cc tigrinc.o translate.o delta.o -o /<>/debian/tmp/usr/bin/delta2maf; chmod 755 /<>/debian/tmp/usr/bin/delta2maf delta2blocks.cc: In function ‘void printAlignments(std::vector, char*, char*, char*, char*)’: delta2blocks.cc:408:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 408 | printf ("%s %s %d %d %d %d ",IdR,IdQ, Ap->sR,Ap->eR,Ap->sQ,Ap->eQ); | ~^ ~~~~~~ | | | | int long int | %ld delta2blocks.cc:408:26: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 408 | printf ("%s %s %d %d %d %d ",IdR,IdQ, Ap->sR,Ap->eR,Ap->sQ,Ap->eQ); | ~^ ~~~~~~ | | | | int long int | %ld delta2blocks.cc:408:29: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 408 | printf ("%s %s %d %d %d %d ",IdR,IdQ, Ap->sR,Ap->eR,Ap->sQ,Ap->eQ); | ~^ ~~~~~~ | | | | int long int | %ld delta2blocks.cc:408:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] 408 | printf ("%s %s %d %d %d %d ",IdR,IdQ, Ap->sR,Ap->eR,Ap->sQ,Ap->eQ); | ~^ ~~~~~~ | | | | int long int | %ld delta2maf.cc: In function ‘void printAlignments(std::vector, char*, char*, std::map, char*>&)’: delta2maf.cc:547:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 547 | printf("a score=%d\n",abs(Ap->eR - Ap->sR)); | ~^ ~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %ld delta2maf.cc:587:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 587 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "-",SeqLenQ); | ~^ ~~~~ | | | | int long int | %ld delta2maf.cc:587:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 587 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "-",SeqLenQ); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:587:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 587 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "-",SeqLenQ); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:590:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 590 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "+",SeqLenQ); | ~^ ~~~~ | | | | int long int | %ld delta2maf.cc:590:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 590 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "+",SeqLenQ); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:590:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 590 | printf("s %s %d %d %s %d ", IdQ, sQ-1, eQ-sQ+1, "+",SeqLenQ); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:597:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 597 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "-",SeqLenR); | ~^ ~~~~ | | | | int long int | %ld delta2maf.cc:597:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 597 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "-",SeqLenR); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:597:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 597 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "-",SeqLenR); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:600:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 600 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "+",SeqLenR); | ~^ ~~~~ | | | | int long int | %ld delta2maf.cc:600:30: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] 600 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "+",SeqLenR); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:600:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=] 600 | printf("s %s %d %d %s %d ", IdR, sR-1, eR-sR+1, "+",SeqLenR); | ~^ ~~~~~~~ | | | | int long int | %ld delta2maf.cc:633:34: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 633 | printf("%s", &Buff2); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:637:34: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 637 | printf("%s", &Buff1); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:659:28: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 659 | printf("%s", &Buff2); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:663:28: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 663 | printf("%s", &Buff1); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:710:30: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 710 | printf("%s", &Buff2); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:714:30: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 714 | printf("%s", &Buff1); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:732:24: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 732 | printf("%s", &Buff2); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* delta2maf.cc:736:24: warning: format ‘%s’ expects argument of type ‘char*’, but argument 2 has type ‘char (*)[(Screen_Width + 1)]’ [-Wformat=] 736 | printf("%s", &Buff1); | ~^ ~~~~~~ | | | | | char (*)[(Screen_Width + 1)] | char* /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now annotate.cc tigrinc.o -o /<>/debian/tmp/usr/bin/annotate; chmod 755 /<>/debian/tmp/usr/bin/annotate /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now combineMUMs.cc tigrinc.o -o /<>/debian/tmp/usr/bin/combineMUMs; chmod 755 /<>/debian/tmp/usr/bin/combineMUMs /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now delta-filter.cc tigrinc.o delta.o -o /<>/debian/tmp/usr/bin/delta-filter; chmod 755 /<>/debian/tmp/usr/bin/delta-filter combineMUMs.cc:26:38: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 26 | #define DEFAULT_ERROR_FILE_NAME "witherrors.gaps" | ^~~~~~~~~~~~~~~~~ combineMUMs.cc:109:27: note: in expansion of macro ‘DEFAULT_ERROR_FILE_NAME’ 109 | char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; | ^~~~~~~~~~~~~~~~~~~~~~~ combineMUMs.cc:135:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 135 | char * Query_Suffix = "Query"; | ^~~~~~~ combineMUMs.cc:145:22: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 145 | char * Ref_Suffix = "Ref"; | ^~~~~ combineMUMs.cc: In function ‘int Read_String(FILE*, char**, long int*, char*)’: combineMUMs.cc:1481:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1481 | fgets (Line, MAX_LINE, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now postnuc.cc tigrinc.o sw_align.o -o /<>/debian/tmp/usr/lib/mummer/postnuc; chmod 755 /<>/debian/tmp/usr/lib/mummer/postnuc /usr/bin/g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now postpro.cc tigrinc.o sw_align.o translate.o -o /<>/debian/tmp/usr/lib/mummer/postpro; chmod 755 /<>/debian/tmp/usr/lib/mummer/postpro make[3]: Leaving directory '/<>/src/tigr' make[2]: Leaving directory '/<>' /usr/bin/make -C docs make[2]: Entering directory '/<>/docs' pdflatex maxmat3man This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./maxmat3man.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-03-14> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (./skaff.sty) (./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file maxmat3man.aux. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) LaTeX Warning: Reference `SecBasicNotions' on page 1 undefined on input line 36 . Overfull \hbox (4.79204pt too wide) in paragraph at lines 60--61 \OT1/ptm/m/n/12 Compute \OT1/ptm/m/it/12 MUM\OT1/ptm/m/n/12 -candidates, i.e. m atches that are unique in the reference-sequence [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] LaTeX Warning: Reference `SecBasicNotions' on page 2 undefined on input line 10 4. [2] [3] Overfull \hbox (8.54073pt too wide) in paragraph at lines 225--225 []\OT1/pcr/m/n/10.95 # ........................................................ ......[] [4] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALL2_BOVIN|ALLERGEN 139 1 155 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALG3_YEAST|PUTATIVE 425 2 904 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALF_TRYBB|FRUCTOSE-BISPHOSPHATE 177 4 794 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_YEAST|ALG11 114 12 599 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALR_SYNY3|ALANINE 354 33 261 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 212 40 991 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 314 41 093 7[] [5] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 360 41 138 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALR_SYNY3|ALANINE 79 44 186 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALP_CEPAC|ALKALINE 366 45 304 7[] [6] [7] (./maxmat3man.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)< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb> Output written on maxmat3man.pdf (7 pages, 134082 bytes). Transcript written on maxmat3man.log. pdflatex maxmat3man This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./maxmat3man.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-03-14> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (./skaff.sty) (./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./maxmat3man.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) Overfull \hbox (4.79204pt too wide) in paragraph at lines 60--61 \OT1/ptm/m/n/12 Compute \OT1/ptm/m/it/12 MUM\OT1/ptm/m/n/12 -candidates, i.e. m atches that are unique in the reference-sequence [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] [2] [3] Overfull \hbox (8.54073pt too wide) in paragraph at lines 225--225 []\OT1/pcr/m/n/10.95 # ........................................................ ......[] [4] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALL2_BOVIN|ALLERGEN 139 1 155 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALG3_YEAST|PUTATIVE 425 2 904 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALF_TRYBB|FRUCTOSE-BISPHOSPHATE 177 4 794 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_YEAST|ALG11 114 12 599 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALR_SYNY3|ALANINE 354 33 261 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 212 40 991 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 314 41 093 7[] [5] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALGB_PSEAE|ALGINATE 360 41 138 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALR_SYNY3|ALANINE 79 44 186 7[] Overfull \hbox (15.11072pt too wide) in paragraph at lines 298--298 [] \OT1/pcr/m/n/10.95 sp|ALP_CEPAC|ALKALINE 366 45 304 7[] [6] [7] (./maxmat3man.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb> Output written on maxmat3man.pdf (7 pages, 133416 bytes). Transcript written on maxmat3man.log. make[2]: Leaving directory '/<>/docs' make[1]: Leaving directory '/<>' dh_auto_test make -j2 check make[1]: Entering directory '/<>' check complete make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp debian/rules override_dh_prep make[1]: Entering directory '/<>' dh_prep -X debian/tmp make[1]: Leaving directory '/<>' debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mv /<>/debian/tmp/usr/bin/annotate /<>/debian/tmp/usr/bin/mummer-annotate make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -Xpdf make[1]: Leaving directory '/<>' dh_fixperms dh_missing dh_dwz -a dwz: debian/mummer/usr/bin/mummer: DWARF compression not beneficial - old size 63125 new size 63381 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mummer' in '../mummer_3.23+dfsg-8_amd64.deb'. dpkg-deb: building package 'mummer-doc' in '../mummer-doc_3.23+dfsg-8_all.deb'. dpkg-deb: building package 'mummer-dbgsym' in '../mummer-dbgsym_3.23+dfsg-8_amd64.deb'. dpkg-genbuildinfo -O../mummer_3.23+dfsg-8_amd64.buildinfo dpkg-genchanges -O../mummer_3.23+dfsg-8_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-06-04T17:06:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mummer_3.23+dfsg-8_amd64.changes: --------------------------------- Format: 1.8 Date: Sun, 04 Dec 2022 12:29:43 +0100 Source: mummer Binary: mummer mummer-dbgsym mummer-doc Architecture: source amd64 all Version: 3.23+dfsg-8 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mummer - Efficient sequence alignment of full genomes mummer-doc - Documentation for MUMmer Closes: 956751 Changes: mummer (3.23+dfsg-8) unstable; urgency=medium . * d/watch: Fix name of upstream tarball * Apply hint by Étienne Mollier to fit current gnuplot version Closes: #956751 * Use secure URI in Homepage field. * Update standards version to 4.6.1, no changes needed. 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664336 mummer_3.23+dfsg-8_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 04 Jun 2024 17:06:51 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-8), bsdutils (= 1:2.40.1-8), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-8), libbrotli1 (= 1.1.0-2+b3), libbsd0 (= 0.12.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), 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2022-12-04 11:29 ./usr/lib/debug/.dwz/x86_64-linux-gnu/mummer.debug drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/share/ drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/doc/mummer-dbgsym -> mummer mummer-doc_3.23+dfsg-8_all.deb ------------------------------ new Debian package, version 2.0. size 1314548 bytes: control archive=2884 bytes. 1113 bytes, 24 lines control 6688 bytes, 76 lines md5sums Package: mummer-doc Source: mummer Version: 3.23+dfsg-8 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 1705 Section: doc Priority: optional Homepage: https://mummer.sourceforge.net/ Description: Documentation for MUMmer MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. . 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Homepage: https://mummer.sourceforge.net/ Description: Efficient sequence alignment of full genomes MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. drwxr-xr-x root/root 0 2022-12-04 11:29 ./ drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/ drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/bin/ -rwxr-xr-x root/root 55656 2022-12-04 11:29 ./usr/bin/combineMUMs -rwxr-xr-x root/root 72088 2022-12-04 11:29 ./usr/bin/delta-filter -rwxr-xr-x root/root 88480 2022-12-04 11:29 ./usr/bin/delta2blocks -rwxr-xr-x root/root 108960 2022-12-04 11:29 ./usr/bin/delta2maf -rwxr-xr-x root/root 26821 2022-12-04 11:29 ./usr/bin/dnadiff -rwxr-xr-x root/root 766 2022-12-04 11:29 ./usr/bin/exact-tandems -rwxr-xr-x root/root 26944 2022-12-04 11:29 ./usr/bin/gaps -rwxr-xr-x root/root 29757 2022-12-04 11:29 ./usr/bin/mapview -rwxr-xr-x root/root 31072 2022-12-04 11:29 ./usr/bin/mgaps -rwxr-xr-x root/root 55376 2022-12-04 11:29 ./usr/bin/mummer -rwxr-xr-x root/root 26944 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./usr/share/doc/mummer/copyright drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/share/doc/mummer/examples/ drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/ -rw-r--r-- root/root 12278 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mapview_0.fig -rw-r--r-- root/root 116949 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mummer.mums -rw-r--r-- root/root 190927 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mummer3.align -rw-r--r-- root/root 53082 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mummer3.errorsgaps -rw-r--r-- root/root 45370 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mummer3.gaps -rw-r--r-- root/root 28238 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/mummer3.out -rw-r--r-- root/root 5110 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/nucmer.coords -rw-r--r-- root/root 2707 2022-12-04 11:29 ./usr/share/doc/mummer/examples/expected/nucmer.delta -rw-r--r-- root/root 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./usr/share/man/man1/nucmer2xfig.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/promer.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/repeat-match.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/run-mummer1.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/run-mummer3.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/show-aligns.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/show-coords.1.gz -> mummer.1.gz -rw-r--r-- root/root 910 2022-12-04 11:29 ./usr/share/man/man1/show-diff.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/show-snps.1.gz -> mummer.1.gz lrwxrwxrwx root/root 0 2022-12-04 11:29 ./usr/share/man/man1/show-tiling.1.gz -> mummer.1.gz drwxr-xr-x root/root 0 2022-12-04 11:29 ./usr/share/perl5/ -rw-r--r-- root/root 54266 2011-12-17 02:49 ./usr/share/perl5/Foundation.pm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 40072 Build-Time: 25 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 35 Job: /srv/debomatic/incoming/mummer_3.23+dfsg-8.dsc Machine Architecture: amd64 Package: mummer Package-Time: 68 Source-Version: 3.23+dfsg-8 Space: 40072 Status: successful Version: 3.23+dfsg-8 -------------------------------------------------------------------------------- Finished at 2024-06-04T17:06:52Z Build needed 00:01:08, 40072k disk space