Wed Apr 8 07:14:13 UTC 2020 I: starting to build progressivemauve/buster/i386 on jenkins on '2020-04-08 07:14' Wed Apr 8 07:14:13 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/4895/console.log Wed Apr 8 07:14:13 UTC 2020 I: Downloading source for buster/progressivemauve=1.2.0+4713+dfsg-4 --2020-04-08 07:14:13-- http://deb.debian.org/debian/pool/main/p/progressivemauve/progressivemauve_1.2.0+4713+dfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2300 (2.2K) Saving to: ‘progressivemauve_1.2.0+4713+dfsg-4.dsc’ 0K .. 100% 187M=0s 2020-04-08 07:14:13 (187 MB/s) - ‘progressivemauve_1.2.0+4713+dfsg-4.dsc’ saved [2300/2300] Wed Apr 8 07:14:13 UTC 2020 I: progressivemauve_1.2.0+4713+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: progressivemauve Binary: progressivemauve Architecture: any Version: 1.2.0+4713+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://darlinglab.org/mauve/user-guide/mauvealigner.html Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/progressivemauve Vcs-Git: https://salsa.debian.org/med-team/progressivemauve.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev Package-List: progressivemauve deb science optional arch=any Checksums-Sha1: 3b09d613f64fa9237d8c0566c02823136a253208 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz c360aa1123bf7f17116c87a3916002507ffbb506 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz Checksums-Sha256: e5f43b4e5af5d6ddb6d4bac91a919d0d2706ff42f51a4209d2d15be8a12c3772 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz 967fc3ede9cabed5d226f680a195cf8381bfe298c66cef6fe307407af99d5daf 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz Files: b9f9a0377aeccaa353cc4a491452003a 96084 progressivemauve_1.2.0+4713+dfsg.orig.tar.xz 0bd30eeadd7194b9b4c88965367c6cc5 17704 progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlwGRKIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFUeA/8Cqrz0ElyD9y6LtHqn+U9+xKK+Y/CBI4T bBbrqS2g+lnH2d4A+fg+j5x2lcNCux/LY7/cerQ6WtlngYJsEmvMxQmsEl6+FCp6 cAq/2iX9nHkhpbY7+I3+n92rJTWPSjjMAivL4fJ0Eu2FOWLY6xzEuIW76GZla8hI VLzPRV8klIDrrMA5Dfr2gSuti4mff5+WaHyemfvk1WOyDEkPNC02M1HCNwochOZ1 R/rM1WunTYDN/KzJiDng2ygYGfn6sJoYDrGNbOtVP6x2F6pXPjFOldKWDO5ZLqwl dX/JW8J53St/obc/+ONMLsIUdIacAhIgueHJcqgIn8WOmZvAA+Q9Z9mX6phQL5mI At8VrlPhwXjAWIxS+/dkHaaBNYKXVlYugK3FTMkdOe4ZXFXEuOzMY812jWZLom+R XEvo5n7AvMuiFgvLKMGcxW1x/uIJcS6c8mEDBXbIPgYT86F8fKHDMjuj4xvQQP+V qGOqgHE5iByU1na0aQd+Pi+F/MDuxmiWbYNgFvl/vvToqKiojGwM1/peIpzhqnGE dkWBZIebjY9AVyaqQJUK0wqI8jWn4hTG0cRmHCA0WcqAJPWvuAN9XAef5kBJfe4Q lj1Xa8c2Y9Piyr0hs7K+uQSxV3132DuSPsEVKLH1IRDpO5M5z3yvFhgmG4wFSIDP zmjEY8njuvc= =n2Uj -----END PGP SIGNATURE----- Wed Apr 8 07:14:13 UTC 2020 I: Checking whether the package is not for us Wed Apr 8 07:14:13 UTC 2020 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Wed Apr 8 07:14:13 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Wed Apr 8 07:21:51 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 7 19:14:15 -12 2020 I: pbuilder-time-stamp: 1586330055 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: using eatmydata during job I: Copying source file I: copying [progressivemauve_1.2.0+4713+dfsg-4.dsc] I: copying [./progressivemauve_1.2.0+4713+dfsg.orig.tar.xz] I: copying [./progressivemauve_1.2.0+4713+dfsg-4.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 Mon Dec 3 21:10:58 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./progressivemauve_1.2.0+4713+dfsg-4.dsc dpkg-source: info: extracting progressivemauve in progressivemauve-1.2.0+4713+dfsg dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg.orig.tar.xz dpkg-source: info: unpacking progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_build.patch dpkg-source: info: applying do_not_build_static_binaries.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying use-native-getopt.patch dpkg-source: info: applying adapt-to-unversioned-libs.patch dpkg-source: info: applying fix_FTBFS_boost1.67.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 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~), pkgconf, libboost-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev, libgenome-dev, libmuscle-dev, libmems-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 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 pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libgenome-dev; however: Package libgenome-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuscle-dev; however: Package libmuscle-dev is not installed. pbuilder-satisfydepends-dummy depends on libmems-dev; however: Package libmems-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-filesystem-dev{a} libboost-filesystem1.67-dev{a} libboost-filesystem1.67.0{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost-system-dev{a} libboost-system1.67-dev{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgenome-dev{a} libgenome0{a} libglib2.0-0{a} libicu-dev{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libmems-dev{a} libmems1{a} libmuscle-dev{a} libmuscle1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkgconf{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 42.7 MB of archives. After unpacking 277 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 icu-devtools i386 63.1-6 [196 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13+deb10u1 [8388 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libboost-dev i386 1.67.0.1 [3864 B] Get: 37 http://deb.debian.org/debian buster/main i386 libboost-filesystem1.67.0 i386 1.67.0-13+deb10u1 [265 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libboost-system1.67-dev i386 1.67.0-13+deb10u1 [232 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libboost-filesystem1.67-dev i386 1.67.0-13+deb10u1 [274 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libboost-filesystem-dev i386 1.67.0.1 [3684 B] Get: 41 http://deb.debian.org/debian buster/main i386 libboost-regex1.67.0 i386 1.67.0-13+deb10u1 [508 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libicu-dev i386 63.1-6 [9374 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libboost-regex1.67-dev i386 1.67.0-13+deb10u1 [561 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libboost-iostreams1.67-dev i386 1.67.0-13+deb10u1 [258 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libboost-iostreams-dev i386 1.67.0.1 [3632 B] Get: 46 http://deb.debian.org/debian buster/main i386 libboost-program-options1.67.0 i386 1.67.0-13+deb10u1 [365 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libboost-program-options1.67-dev i386 1.67.0-13+deb10u1 [395 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libboost-program-options-dev i386 1.67.0.1 [3660 B] Get: 49 http://deb.debian.org/debian buster/main i386 libboost-system-dev i386 1.67.0.1 [3788 B] Get: 50 http://deb.debian.org/debian buster/main i386 libgenome0 i386 1.3.11+svn20110227.4616-2 [130 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libgenome-dev i386 1.3.11+svn20110227.4616-2 [202 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libmuscle1 i386 3.7+4565-6 [236 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libmems1 i386 1.6.0+4725-8+b1 [633 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libmuscle-dev i386 3.7+4565-6 [290 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libmems-dev i386 1.6.0+4725-8+b1 [928 kB] Get: 56 http://deb.debian.org/debian buster/main i386 pkgconf i386 1.6.0-1 [69.7 kB] Fetched 42.7 MB in 19s (2201 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6_i386.deb ... Unpacking libicu63:i386 (63.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../33-icu-devtools_63.1-6_i386.deb ... Unpacking icu-devtools (63.1-6) ... Selecting previously unselected package libboost1.67-dev:i386. Preparing to unpack .../34-libboost1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../35-libboost-dev_1.67.0.1_i386.deb ... Unpacking libboost-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-filesystem1.67.0:i386. Preparing to unpack .../36-libboost-filesystem1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-filesystem1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system1.67-dev:i386. Preparing to unpack .../37-libboost-system1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-system1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67-dev:i386. Preparing to unpack .../38-libboost-filesystem1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-filesystem1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem-dev:i386. Preparing to unpack .../39-libboost-filesystem-dev_1.67.0.1_i386.deb ... Unpacking libboost-filesystem-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-regex1.67.0:i386. Preparing to unpack .../40-libboost-regex1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-regex1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libicu-dev:i386. Preparing to unpack .../41-libicu-dev_63.1-6_i386.deb ... Unpacking libicu-dev:i386 (63.1-6) ... Selecting previously unselected package libboost-regex1.67-dev:i386. Preparing to unpack .../42-libboost-regex1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-regex1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams1.67-dev:i386. Preparing to unpack .../43-libboost-iostreams1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-iostreams1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-iostreams-dev:i386. Preparing to unpack .../44-libboost-iostreams-dev_1.67.0.1_i386.deb ... Unpacking libboost-iostreams-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-program-options1.67.0:i386. Preparing to unpack .../45-libboost-program-options1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-program-options1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options1.67-dev:i386. Preparing to unpack .../46-libboost-program-options1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-program-options1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options-dev:i386. Preparing to unpack .../47-libboost-program-options-dev_1.67.0.1_i386.deb ... Unpacking libboost-program-options-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-system-dev:i386. Preparing to unpack .../48-libboost-system-dev_1.67.0.1_i386.deb ... Unpacking libboost-system-dev:i386 (1.67.0.1) ... Selecting previously unselected package libgenome0:i386. Preparing to unpack .../49-libgenome0_1.3.11+svn20110227.4616-2_i386.deb ... Unpacking libgenome0:i386 (1.3.11+svn20110227.4616-2) ... Selecting previously unselected package libgenome-dev. Preparing to unpack .../50-libgenome-dev_1.3.11+svn20110227.4616-2_i386.deb ... Unpacking libgenome-dev (1.3.11+svn20110227.4616-2) ... Selecting previously unselected package libmuscle1. Preparing to unpack .../51-libmuscle1_3.7+4565-6_i386.deb ... Unpacking libmuscle1 (3.7+4565-6) ... Selecting previously unselected package libmems1:i386. Preparing to unpack .../52-libmems1_1.6.0+4725-8+b1_i386.deb ... Unpacking libmems1:i386 (1.6.0+4725-8+b1) ... Selecting previously unselected package libmuscle-dev. Preparing to unpack .../53-libmuscle-dev_3.7+4565-6_i386.deb ... Unpacking libmuscle-dev (3.7+4565-6) ... Selecting previously unselected package libmems-dev. Preparing to unpack .../54-libmems-dev_1.6.0+4725-8+b1_i386.deb ... Unpacking libmems-dev (1.6.0+4725-8+b1) ... Selecting previously unselected package pkgconf. Preparing to unpack .../55-pkgconf_1.6.0-1_i386.deb ... Adding 'diversion of /usr/bin/pkg-config to /usr/bin/pkg-config.real by pkgconf' Adding 'diversion of /usr/share/aclocal/pkg.m4 to /usr/share/aclocal/pkg.real.m4 by pkgconf' Adding 'diversion of /usr/share/man/man1/pkg-config.1.gz to /usr/share/man/man1/pkg-config.real.1.gz by pkgconf' Adding 'diversion of /usr/share/pkg-config-crosswrapper to /usr/share/pkg-config-crosswrapper.real by pkgconf' Unpacking pkgconf (1.6.0-1) ... Setting up libboost1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libboost-program-options1.67.0:i386 (1.67.0-13+deb10u1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libgenome0:i386 (1.3.11+svn20110227.4616-2) ... Setting up libmuscle1 (3.7+4565-6) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libgenome-dev (1.3.11+svn20110227.4616-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libboost-program-options1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6) ... Setting up pkgconf (1.6.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:i386 (1.67.0.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libmuscle-dev (3.7+4565-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libboost-filesystem1.67.0:i386 (1.67.0-13+deb10u1) ... Setting up libboost-system1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libboost-dev:i386 (1.67.0.1) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libicu-dev:i386 (63.1-6) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libboost-regex1.67.0:i386 (1.67.0-13+deb10u1) ... Setting up libboost-filesystem1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libboost-system-dev:i386 (1.67.0.1) ... Setting up m4 (1.4.18-2) ... Setting up libmems1:i386 (1.6.0+4725-8+b1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libboost-iostreams1.67-dev:i386 (1.67.0-13+deb10u1) ... Setting up libboost-filesystem-dev:i386 (1.67.0.1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libmems-dev (1.6.0+4725-8+b1) ... Setting up libboost-iostreams-dev:i386 (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/progressivemauve-1.2.0+4713+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 progressivemauve dpkg-buildpackage: info: source version 1.2.0+4713+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:21: installing 'config/compile' configure.ac:9: installing 'config/config.guess' configure.ac:9: installing 'config/config.sub' configure.ac:11: installing 'config/install-sh' configure.ac:11: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am:12: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') src/Makefile.am: installing 'config/depcomp' src/Makefile.am:51: warning: variable 'EXTRA_mauveStatic_SOURCES' is defined but no program or src/Makefile.am:51: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:49: warning: variable 'mauveStatic_SOURCES' is defined but no program or src/Makefile.am:49: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:160: warning: variable 'progressiveMauveStatic_SOURCES' is defined but no program or src/Makefile.am:160: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:50: warning: variable 'mauveStatic_LDADD' is defined but no program or src/Makefile.am:50: library has 'mauveStatic' as canonical name (possible typo) src/Makefile.am:161: warning: variable 'progressiveMauveStatic_LDADD' is defined but no program or src/Makefile.am:161: library has 'progressiveMauveStatic' as canonical name (possible typo) src/Makefile.am:52: warning: variable 'mauveStatic_DEPENDENCIES' is defined but no program or src/Makefile.am:52: library has 'mauveStatic' as canonical name (possible typo) dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking whether ln -s works... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for getopt_long... yes checking for getopt... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking for memset... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking libintl.h usability... yes checking libintl.h presence... yes checking for libintl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... yes checking whether gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j10 make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making all in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make all-am make[3]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveAligner.o mauveAligner.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scoreAlignment.o scoreAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniqueMerCount.o uniqueMerCount.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toRawSequence.o toRawSequence.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mfa2xmfa.o mfa2xmfa.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o addUnalignedIntervals.o addUnalignedIntervals.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toMultiFastA.o toMultiFastA.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getAlignmentWindows.o getAlignmentWindows.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o uniquifyTrees.o uniquifyTrees.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o toGrimmFormat.o toGrimmFormat.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from mauveAligner.cpp:30: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ mauveAligner.cpp:413:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ mauveAligner.cpp:413:70: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] cerr << "mauveAligner " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getAlignmentWindows.cpp:14: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from toMultiFastA.cpp:2: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from addUnalignedIntervals.cpp:2: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mauveToXMFA.o mauveToXMFA.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripGapColumns.o stripGapColumns.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o progressiveMauve.o progressiveMauve.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from progressiveMauve.cpp:26: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ progressiveMauve.cpp:417:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ progressiveMauve.cpp:417:74: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] cerr << "progressiveMauve " << " build date " << __DATE__ << " at " << __TIME__ << endl; ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o UniqueMatchFinder.o UniqueMatchFinder.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o extractBCITrees.o extractBCITrees.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o createBackboneMFA.o createBackboneMFA.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o repeatoire.o repeatoire.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignmentProjector.o alignmentProjector.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from createBackboneMFA.cpp:2: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stripSubsetLCBs.o stripSubsetLCBs.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o projectAndStrip.o projectAndStrip.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from repeatoire.cpp:4: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o makeBadgerMatrix.o makeBadgerMatrix.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from alignmentProjector.cpp:18: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o randomGeneSample.o randomGeneSample.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getOrthologList.o getOrthologList.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from projectAndStrip.cpp:18: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from randomGeneSample.cpp:18: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from getOrthologList.cpp:18: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbFilter.o bbFilter.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbFilter.cpp:1: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bbAnalyze.o bbAnalyze.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from bbAnalyze.cpp:4: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o backbone_global_to_local.o backbone_global_to_local.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o xmfa2maf.o xmfa2maf.cpp g++ -DHAVE_CONFIG_H -I. -I/usr/include/libMems -I/usr/include/libGenome -I/usr/include/libMUSCLE -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o coordinateTranslate.o coordinateTranslate.cpp In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/Backbone.h:24, from backbone_global_to_local.cpp:2: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ In file included from /usr/include/c++/8/ext/hash_map:60, from /usr/include/libMems/HomologyHMM/dptables.h:43, from /usr/include/libMems/HomologyHMM/homology.h:27, from /usr/include/libMems/Islands.h:25, from /usr/include/libMems/ProgressiveAligner.h:21, from xmfa2maf.cpp:2: /usr/include/c++/8/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -Wl,-z,relro -Wl,-z,now -o mauveAligner mauveAligner.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o scoreAlignment scoreAlignment.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniqueMerCount uniqueMerCount.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toRawSequence toRawSequence.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mfa2xmfa mfa2xmfa.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o addUnalignedIntervals addUnalignedIntervals.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toMultiFastA toMultiFastA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getAlignmentWindows getAlignmentWindows.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o uniquifyTrees uniquifyTrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o toGrimmFormat toGrimmFormat.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o mauveToXMFA mauveToXMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripGapColumns stripGapColumns.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o progressiveMauve progressiveMauve.o UniqueMatchFinder.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o extractBCITrees extractBCITrees.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o createBackboneMFA createBackboneMFA.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o alignmentProjector alignmentProjector.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o stripSubsetLCBs stripSubsetLCBs.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o projectAndStrip projectAndStrip.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o makeBadgerMatrix makeBadgerMatrix.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o randomGeneSample randomGeneSample.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbFilter bbFilter.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o getOrthologList getOrthologList.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o coordinateTranslate coordinateTranslate.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o backbone_global_to_local backbone_global_to_local.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o xmfa2maf xmfa2maf.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o bbAnalyze bbAnalyze.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -DCOMMAND_LINE -g -O2 -ffile-prefix-map=/build/progressivemauve-1.2.0+4713+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -Wl,-z,relro -Wl,-z,now -o repeatoire repeatoire.o -lMems -lboost_system -lboost_filesystem -lboost_program_options -lboost_iostreams -lrt -lpthread -lGenome -lMUSCLE make[3]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making check in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 install DESTDIR=/build/progressivemauve-1.2.0\+4713\+dfsg/debian/progressivemauve AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' Making install in src make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' /usr/bin/install -c mauveAligner scoreAlignment uniqueMerCount toRawSequence mfa2xmfa addUnalignedIntervals toMultiFastA getAlignmentWindows uniquifyTrees toGrimmFormat mauveToXMFA stripGapColumns progressiveMauve extractBCITrees createBackboneMFA repeatoire alignmentProjector stripSubsetLCBs projectAndStrip makeBadgerMatrix randomGeneSample getOrthologList bbFilter bbAnalyze backbone_global_to_local xmfa2maf coordinateTranslate '/build/progressivemauve-1.2.0+4713+dfsg/debian/progressivemauve/usr/bin' make[3]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg/src' make[2]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[3]: Entering directory '/build/progressivemauve-1.2.0+4713+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[2]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' make[1]: Leaving directory '/build/progressivemauve-1.2.0+4713+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/stripSubsetLCBs were not linked against libMUSCLE.so.1 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/stripSubsetLCBs were not linked against libpthread.so.0 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/progressivemauve/usr/bin/createBackboneMFA debian/progressivemauve/usr/bin/uniquifyTrees debian/progressivemauve/usr/bin/toGrimmFormat debian/progressivemauve/usr/bin/uniqueMerCount debian/progressivemauve/usr/bin/alignmentProjector debian/progressivemauve/usr/bin/backbone_global_to_local debian/progressivemauve/usr/bin/toRawSequence debian/progressivemauve/usr/bin/bbAnalyze debian/progressivemauve/usr/bin/mauveAligner debian/progressivemauve/usr/bin/xmfa2maf debian/progressivemauve/usr/bin/toMultiFastA debian/progressivemauve/usr/bin/bbFilter debian/progressivemauve/usr/bin/projectAndStrip debian/progressivemauve/usr/bin/repeatoire debian/progressivemauve/usr/bin/getAlignmentWindows debian/progressivemauve/usr/bin/mauveToXMFA debian/progressivemauve/usr/bin/coordinateTranslate debian/progressivemauve/usr/bin/extractBCITrees debian/progressivemauve/usr/bin/scoreAlignment debian/progressivemauve/usr/bin/randomGeneSample debian/progressivemauve/usr/bin/makeBadgerMatrix debian/progressivemauve/usr/bin/addUnalignedIntervals debian/progressivemauve/usr/bin/stripGapColumns debian/progressivemauve/usr/bin/getOrthologList debian/progressivemauve/usr/bin/progressiveMauve debian/progressivemauve/usr/bin/mfa2xmfa debian/progressivemauve/usr/bin/stripSubsetLCBs were not linked against librt.so.1 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'progressivemauve-dbgsym' in '../progressivemauve-dbgsym_1.2.0+4713+dfsg-4_i386.deb'. dpkg-deb: building package 'progressivemauve' in '../progressivemauve_1.2.0+4713+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../progressivemauve_1.2.0+4713+dfsg-4_i386.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/28284 and its subdirectories I: Current time: Tue Apr 7 19:21:50 -12 2020 I: pbuilder-time-stamp: 1586330510 Wed Apr 8 07:21:52 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build16-i386.debian.net. Wed Apr 8 07:21:52 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build16-i386.debian.net. Wed Apr 8 07:23:11 UTC 2020 I: Deleting $TMPDIR on profitbricks-build16-i386.debian.net. Wed Apr 8 07:23:12 UTC 2020 I: progressivemauve_1.2.0+4713+dfsg-4_i386.changes: Format: 1.8 Date: Tue, 04 Dec 2018 10:03:31 +0100 Source: progressivemauve Binary: progressivemauve progressivemauve-dbgsym Architecture: i386 Version: 1.2.0+4713+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: progressivemauve - multiple genome alignment algorithms Closes: 914049 Changes: progressivemauve (1.2.0+4713+dfsg-4) unstable; urgency=medium . [ Giovanni Mascellani ] * Fix FTBFS with boost1.67 Closes: #914049 . [ Andreas Tille ] * Standards-Version: 4.2.1 Checksums-Sha1: db8a04736677f187512574660e91dafbb6ce6eb3 18641744 progressivemauve-dbgsym_1.2.0+4713+dfsg-4_i386.deb e05251affc6f96ab0b9e3511bb381141dbce115f 5738 progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo 310180e45961087f7fc99458401660920329c270 839928 progressivemauve_1.2.0+4713+dfsg-4_i386.deb Checksums-Sha256: 213db33347975ac7bb89fea9168bace97b526f6a77175b845857db98a179807d 18641744 progressivemauve-dbgsym_1.2.0+4713+dfsg-4_i386.deb f54db4f47d1d3395875c31951acd910d19a3f5e45cf3ee93d6077228dd2bb591 5738 progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo f7e0e4a21b6808faaddf1d4283c23510e531bf88b0b78966f1d807b57da73fa8 839928 progressivemauve_1.2.0+4713+dfsg-4_i386.deb Files: 9636993f62f752bdb9d7f23af55d1689 18641744 debug optional progressivemauve-dbgsym_1.2.0+4713+dfsg-4_i386.deb ce8e267fcd53c3d47382b9032feec0ce 5738 science optional progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo bb71726ec63fb2f78061aa9d62853564 839928 science optional progressivemauve_1.2.0+4713+dfsg-4_i386.deb Wed Apr 8 07:23:22 UTC 2020 I: diffoscope 137 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.dPE8kd3DCH/progressivemauve_1.2.0+4713+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.dPE8kd3DCH/progressivemauve_1.2.0+4713+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.dPE8kd3DCH/progressivemauve_1.2.0+4713+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.dPE8kd3DCH/b1/progressivemauve_1.2.0+4713+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/tmp.dPE8kd3DCH/b2/progressivemauve_1.2.0+4713+dfsg-4_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.251s) 1.251s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.495s) 0.495s 10 calls diffoscope.comparators.binary.FilesystemFile Wed Apr 8 07:23:44 UTC 2020 I: diffoscope 137 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 8 07:23:44 UTC 2020 I: progressivemauve from buster built successfully and reproducibly on i386. Wed Apr 8 07:23:46 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Apr 8 07:23:46 UTC 2020 I: Submitting 8.0K b1/progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo.asc Wed Apr 8 07:23:48 UTC 2020 I: Submitting 8.0K b2/progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo.asc Wed Apr 8 07:23:49 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 8 07:23:49 UTC 2020 I: Done submitting .buildinfo files. Wed Apr 8 07:23:49 UTC 2020 I: Removing signed progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo.asc files: removed './b1/progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo.asc' removed './b2/progressivemauve_1.2.0+4713+dfsg-4_i386.buildinfo.asc'