sbuild (Debian sbuild) 0.78.1 (09 February 2019) on 36857dea695f +==============================================================================+ | probalign 1.4-8 (armhf) Thu, 07 Mar 2019 21:52:12 +0000 | +==============================================================================+ Package: probalign Version: 1.4-8 Source Version: 1.4-8 Distribution: unstable-amd64-sbuild Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-c6011cb9-4da4-472b-bd0a-f1340002aca6' with '<>' I: NOTICE: Log filtering will replace 'build/probalign-kxx8k6/resolver-tBPPZI' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://cdn-fastly.deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /home/build/sbuild-setup/repo/pool/main/p/probalign/probalign_1.4-8.dsc exists in /home/build/sbuild-setup/repo/pool/main/p/probalign; copying to chroot I: NOTICE: Log filtering will replace 'build/probalign-kxx8k6/probalign-1.4' with '<>' I: NOTICE: Log filtering will replace 'build/probalign-kxx8k6' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), help2man, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper (>= 11~), help2man, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [400 B] Get:5 copy:/<>/apt_archive ./ Packages [491 B] Fetched 1848 B in 0s (133 kB/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 packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libglib2.0-0 libgomp1:armhf libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:armhf libstdc++6:armhf libtool libubsan1:armhf libuchardet0 linux-libc-dev:armhf m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf 0 upgraded, 41 newly installed, 0 to remove and 0 not upgraded. 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Unpacking sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-1) ... No schema files found: doing nothing. Setting up linux-libc-dev:armhf (4.19.20-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up help2man (1.47.8) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up gcc-8-base:armhf (8.3.0-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1) ... Setting up libfile-stripnondeterminism-perl (1.1.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... 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 autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... 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 po-debconf (1.0.21) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:armhf (2.28-8) ... Setting up libc6-dev:armhf (2.28-8) ... Setting up libgcc1:armhf (1:8.3.0-2) ... Setting up libgomp1:armhf (8.3.0-2) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:armhf (8.3.0-2) ... Setting up dh-strip-nondeterminism (1.1.1-1) ... Setting up libstdc++6:armhf (8.3.0-2) ... Setting up debhelper (12.1.1) ... Setting up libasan5:armhf (8.3.0-2) ... 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Updating symlinks in /usr/lib/ccache ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Initial Foreign Architectures: armhf Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 3.16.0-4-amd64 #1 SMP Debian 3.16.51-3 (2017-12-13) amd64 (x86_64) Toolchain package versions: binutils_2.31.1-15 dpkg-dev_1.19.5 g++-8_8.3.0-2 gcc-8_8.3.0-2 libc6-dev_2.28-8 libstdc++-8-dev_8.3.0-2 libstdc++-8-dev-armhf-cross_8.3.0-2cross1 libstdc++6_8.3.0-2 libstdc++6-armhf-cross_8.3.0-2cross1 linux-libc-dev_4.19.20-1 Package versions: adduser_3.118 apt_1.8.0~rc4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.46 bash_5.0-2 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MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: probalign Binary: probalign Architecture: any Version: 1.4-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://probalign.njit.edu/standalone.html Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/probalign Vcs-Git: https://salsa.debian.org/med-team/probalign.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), help2man Package-List: probalign deb science optional arch=any Checksums-Sha1: b03b52e084da024780dfe051213c11e664592aeb 30060 probalign_1.4.orig.tar.gz 5403a35d9956ef3bd8491c020b7583ad051c684d 4676 probalign_1.4-8.debian.tar.xz Checksums-Sha256: b221a27c5cbc3e5c707b0514c71301806074a2bf54047b57bd2d40497b663c29 30060 probalign_1.4.orig.tar.gz a2377431e484fcb0956386b93cb16c678a94b488c16992229db0de8677fcd7c3 4676 probalign_1.4-8.debian.tar.xz Files: 255d6ab775867a54d3727764b8dff561 30060 probalign_1.4.orig.tar.gz 2887241bf5e380060124f94aacb78947 4676 probalign_1.4-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlvR1GwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG3MA/+LiZRDDhT7o2U9GoVOdUaEpnWflWns8wL l3tTcCTcF0mlgEFxvSx9RQOMG6UgI3rKPWmaTXQ7JRqr9OmifNTw1WBGUTVK8cax Vuk3hsvjyt1Ais33/xr+WRD0/ob9QycXdQvfdLNj26KBtUxUozgYIDX1o/bnrQsM lTh8oQWkNcPPzAs0R5ilR4kMJtL865VXuoG4RFflNDuOe+RdDcNscRkC42RNzd5U mRWJ5evA2MSxg2F6jb8xXLYvdkwB7+dfiI8BrdBf2kvE3c9Ekl7qHtIFnHOAt6Wq HiFeP1PB6qyXi02l4znfBeASk5qUSK/IbYwesx9Egfe3EbxFKUfoVN40FGSKFQpJ yvQGTRkZVbZgYuLLn/Esf0WrGqt4LX8d2wwoxd3iFJxkK5hu06iqw2l3fyRJvm4s OFtL+FRAHcsvvgk/O7eLjtEJ+CbbpjMDQSGOKslqSuwndexrPleGLjaluHiCIqwA 6O/LVkRdVdIGGIRnf6WDM44j8AM4d97jO5Br1omGPjyD8kzJ7sUlToUd/F99rhwV cJPhYqBm8Y6+4rseV6mfxQTvFJ/I7aruxITvvI428RGewCtTuJgIDOgG83WS43Yn mvTz2/AMgkPQ6gNUSPxsGhimQ2LXfFAzF+lPJ6F4G2k2ATtkS0BUrVU8gDtMRx7c 2R1fL/+mc0o= =EqZi -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 25 14:34:20 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./probalign_1.4-8.dsc dpkg-source: info: extracting probalign in /<> dpkg-source: info: unpacking probalign_1.4.orig.tar.gz dpkg-source: info: unpacking probalign_1.4-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_fixes.patch dpkg-source: info: applying fix-gcc-4.6.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CCACHE_COMPRESS=1 CCACHE_DIR=/var/cache/ccache-sbuild CCACHE_UMASK=002 CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=build PATH=/usr/lib/ccache:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=build SCHROOT_SESSION_ID=unstable-amd64-sbuild-c6011cb9-4da4-472b-bd0a-f1340002aca6 SCHROOT_UID=1000 SCHROOT_USER=build SHELL=/bin/sh USER=build dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot -j16 dpkg-buildpackage: info: source package probalign dpkg-buildpackage: info: source version 1.4-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j16 clean make[1]: Entering directory '/<>' rm -f probalign make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j16 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc make[1]: Entering directory '/<>' arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -W -Wall -funroll-loops -lm -o probalign Main.cc PostProbs.cc ComputeAlignment.cc ReadMatrix.cc -Wl,-z,relro -Wl,-z,now PostProbs.cc: In function ‘VF* revers_partf(long double**, float, float, float)’: PostProbs.cc:312:17: warning: variable ‘zz’ set but not used [-Wunused-but-set-variable] long double zz = 0; ^~ PostProbs.cc: In function ‘VF* ComputePostProbs(int, int, std::__cxx11::string, std::__cxx11::string)’: PostProbs.cc:892:9: warning: variable ‘stock_loop’ set but not used [-Wunused-but-set-variable] int stock_loop = 1; ^~~~~~~~~~ make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' help2man --name="Align sequences in MFAFILE(s) and print result to standard output" \ --no-discard-stderr \ --version-string=1.4 \ --help-option=" " \ --no-info \ /<>/probalign > /<>/debian/probalign/usr/share/man/man1/probalign.1 make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/probalign/usr/bin/probalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'probalign-dbgsym' in '../probalign-dbgsym_1.4-8_armhf.deb'. dpkg-deb: building package 'probalign' in '../probalign_1.4-8_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../probalign_1.4-8_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-03-07T21:52:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ probalign_1.4-8_armhf.changes: ------------------------------ Format: 1.8 Date: Tue, 23 Oct 2018 19:16:37 +0200 Source: probalign Binary: probalign probalign-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.4-8 Distribution: unstable-amd64-sbuild Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: probalign - multiple sequence alignment using partition function posterior pr Changes: probalign (1.4-8) unstable; urgency=medium . * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 520610bac2f9595c08ec09ffc360abce1b9708f4 529620 probalign-dbgsym_1.4-8_armhf.deb fb05feba092a694008944b64af15ba0376bbc9a4 4535 probalign_1.4-8_armhf.buildinfo b2295aa78b0a245208342972e9fd9613bee9b4d0 54112 probalign_1.4-8_armhf.deb Checksums-Sha256: c93f7c1f949a3281bb33a8b6ce2626b5c9d159a6d7c8268d448149a35cce0814 529620 probalign-dbgsym_1.4-8_armhf.deb b22f781cad562c02f0f01bc686e3ad8008c588e7fb5ace191dce18f29a001649 4535 probalign_1.4-8_armhf.buildinfo 66d515e59ccabde0a55c4812d2384fe57abfd602d55e9930ed073741e6f78f36 54112 probalign_1.4-8_armhf.deb Files: f8ffe21229111d7a7776cfc79c30d6ff 529620 debug optional probalign-dbgsym_1.4-8_armhf.deb d176971c7b2314aab63106c2a386e366 4535 science optional probalign_1.4-8_armhf.buildinfo 9a1933a2c774d74f50a573866ed05aa6 54112 science optional probalign_1.4-8_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: probalign Binary: probalign Architecture: armhf Version: 1.4-8 Checksums-Md5: f8ffe21229111d7a7776cfc79c30d6ff 529620 probalign-dbgsym_1.4-8_armhf.deb 9a1933a2c774d74f50a573866ed05aa6 54112 probalign_1.4-8_armhf.deb Checksums-Sha1: 520610bac2f9595c08ec09ffc360abce1b9708f4 529620 probalign-dbgsym_1.4-8_armhf.deb b2295aa78b0a245208342972e9fd9613bee9b4d0 54112 probalign_1.4-8_armhf.deb Checksums-Sha256: c93f7c1f949a3281bb33a8b6ce2626b5c9d159a6d7c8268d448149a35cce0814 529620 probalign-dbgsym_1.4-8_armhf.deb 66d515e59ccabde0a55c4812d2384fe57abfd602d55e9930ed073741e6f78f36 54112 probalign_1.4-8_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 07 Mar 2019 21:52:36 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 10.1), base-passwd (= 3.5.46), bash (= 5.0-2), binutils (= 2.31.1-15), binutils-common (= 2.31.1-15), binutils-x86-64-linux-gnu (= 2.31.1-15), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.33.1-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-2), dash (= 0.5.10.2-5), debconf (= 1.5.71), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.1-1), diffutils (= 1:3.7-2), dpkg (= 1.19.5), dpkg-dev (= 1.19.5), dwz (= 0.12-3), fdisk (= 2.33.1-0.1), file (= 1:5.35-4), findutils (= 4.6.0+git+20190209-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-2), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-2), gcc-8-base (= 8.3.0-2), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), help2man (= 1.47.8), hostname (= 3.21), init-system-helpers (= 1.56+nmu1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.64-1), libasan5 (= 8.3.0-2), libatomic1 (= 8.3.0-2), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-2), libaudit1 (= 1:2.8.4-2), libbinutils (= 2.31.1-15), libblkid1 (= 2.33.1-0.1), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-8), libc-dev-bin (= 2.28-8), libc6 (= 2.28-8), libc6-dev (= 2.28-8), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-2), libcroco3 (= 0.6.12-3), libdb5.3 (= 5.3.28+dfsg1-0.5), libdebconfclient0 (= 0.248), libdpkg-perl (= 1.19.5), libelf1 (= 0.176-1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.1-1), libgcc-8-dev (= 8.3.0-2), libgcc1 (= 1:8.3.0-2), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-3), libgdbm6 (= 1.18.1-3), libglib2.0-0 (= 2.58.3-1), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 8.3.0-2), libgpg-error0 (= 1.35-1), libicu63 (= 63.1-6), libisl19 (= 0.20-2), libitm1 (= 8.3.0-2), liblocale-gettext-perl (= 1.07-3+b4), liblsan0 (= 8.3.0-2), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.35-4), libmagic1 (= 1:5.35-4), libmount1 (= 2.33.1-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-2), libncurses6 (= 6.1+20181013-2), libncursesw6 (= 6.1+20181013-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre3 (= 2:8.39-12), libperl5.28 (= 5.28.1-4), libpipeline1 (= 1.5.1-2), libquadmath0 (= 8.3.0-2), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.33.1-0.1), libstdc++-8-dev (= 8.3.0-2), libstdc++6 (= 8.3.0-2), libsystemd0 (= 241-1), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-2), libubsan1 (= 8.3.0-2), libuchardet0 (= 0.0.6-3), libudev1 (= 241-1), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 4.19.20-1), login (= 1:4.5-1.1), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.5-2), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20181013-2), ncurses-bin (= 6.1+20181013-2), patch (= 2.7.6-3), perl (= 5.28.1-4), perl-base (= 5.28.1-4), perl-modules-5.28 (= 5.28.1-4), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.93-8), tar (= 1.30+dfsg-5), util-linux (= 2.33.1-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=16" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" MAKEFLAGS=" -j16" SOURCE_DATE_EPOCH="1540314997" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ probalign-dbgsym_1.4-8_armhf.deb -------------------------------- new Debian package, version 2.0. size 529620 bytes: control archive=532 bytes. 374 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: probalign-dbgsym Source: probalign Version: 1.4-8 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 544 Depends: probalign (= 1.4-8) Section: debug Priority: optional Description: debug symbols for probalign Build-Ids: cb40841923771ca56e70a85d95fe246105797a6a drwxr-xr-x root/root 0 2018-10-23 17:16 ./ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/lib/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/lib/debug/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/lib/debug/.build-id/cb/ -rw-r--r-- root/root 546152 2018-10-23 17:16 ./usr/lib/debug/.build-id/cb/40841923771ca56e70a85d95fe246105797a6a.debug drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-10-23 17:16 ./usr/share/doc/probalign-dbgsym -> probalign probalign_1.4-8_armhf.deb ------------------------- new Debian package, version 2.0. size 54112 bytes: control archive=1160 bytes. 1060 bytes, 20 lines control 621 bytes, 9 lines md5sums Package: probalign Version: 1.4-8 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 110 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://probalign.njit.edu/standalone.html Description: multiple sequence alignment using partition function posterior probabilities Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading alignment programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequences. On heteregeneous length datasets containing repeats Probalign alignment accuracy is 10% and 15% higher than the other three methods when standard deviation of length is at least 300 and 400. drwxr-xr-x root/root 0 2018-10-23 17:16 ./ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/bin/ -rwxr-xr-x root/root 93016 2018-10-23 17:16 ./usr/bin/probalign drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/doc/probalign/ -rw-r--r-- root/root 2679 2010-11-23 17:11 ./usr/share/doc/probalign/README -rw-r--r-- root/root 262 2018-10-23 17:16 ./usr/share/doc/probalign/README.test -rw-r--r-- root/root 875 2018-10-23 17:16 ./usr/share/doc/probalign/changelog.Debian.gz -rw-r--r-- root/root 983 2018-10-23 17:16 ./usr/share/doc/probalign/copyright -rw-r--r-- root/root 365 2018-10-23 17:16 ./usr/share/doc/probalign/run-unit-test -rw-r--r-- root/root 531 2018-10-23 17:16 ./usr/share/doc/probalign/test_data_n.fas -rw-r--r-- root/root 453 2018-10-23 17:16 ./usr/share/doc/probalign/test_data_p.fas drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/man/ drwxr-xr-x root/root 0 2018-10-23 17:16 ./usr/share/man/man1/ -rw-r--r-- root/root 280 2018-10-23 17:16 ./usr/share/man/man1/probalign.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [531 B] Get:5 copy:/<>/apt_archive ./ Packages [618 B] Fetched 2112 B in 0s (179 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: diffstat libapt-pkg-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libio-async-perl libio-pty-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libparse-debianchangelog-perl libpath-tiny-perl libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl lintian patchutils t1utils Suggested packages: libhtml-template-perl binutils-multiarch libtext-template-perl Recommended packages: libcgi-fast-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat libapt-pkg-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libio-async-perl libio-pty-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libparse-debianchangelog-perl libpath-tiny-perl libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl lintian patchutils sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. Need to get 2847 kB/2971 kB of archives. After this operation, 9356 kB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:5 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:6 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:7 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:8 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:9 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:10 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:11 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:12 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:13 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:14 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:15 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:16 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:17 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:18 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:19 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:20 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:21 http://cdn-fastly.deb.debian.org/debian sid/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:22 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:23 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:24 http://cdn-fastly.deb.debian.org/debian sid/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:25 http://cdn-fastly.deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:26 http://cdn-fastly.deb.debian.org/debian sid/main amd64 lintian all 2.9.1 [1193 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2847 kB in 6s (471 kB/s) Selecting previously unselected package diffstat. (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../01-libapt-pkg-perl_0.1.34+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.34+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../02-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../03-libcgi-pm-perl_4.40-1_all.deb ... Unpacking libcgi-pm-perl (4.40-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../04-libsub-name-perl_0.21-1+b3_amd64.deb ... Unpacking libsub-name-perl (0.21-1+b3) ... Selecting previously unselected package libclass-accessor-perl. Preparing to unpack .../05-libclass-accessor-perl_0.51-1_all.deb ... 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Setting up libstruct-dumb-perl (0.09-1) ... Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libfuture-perl (0.39-1) ... Setting up libcgi-pm-perl (4.40-1) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libio-async-perl (0.72-1) ... Setting up patchutils (0.3.4-2) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up diffstat (1.62-1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libnet-dns-perl (1.19-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up lintian (2.9.1) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl uuid-runtime Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libauthen-sasl-perl libdata-dump-perl libfont-afm-perl libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libmailtools-perl libnet-smtp-ssl-perl libyaml-0-2 libyaml-libyaml-perl uuid-runtime Use 'apt autoremove' to remove them. The following packages will be REMOVED: autoconf* automake* autopoint* autotools-dev* bsdmainutils* debhelper* dh-autoreconf* dh-strip-nondeterminism* diffstat* dwz* gcc-8-base:armhf* gettext* gettext-base* groff-base* help2man* intltool-debian* libapt-pkg-perl* libarchive-zip-perl* libasan5:armhf* libatomic1:armhf* libbsd0* libc6:armhf* libc6-dev:armhf* libcapture-tiny-perl* libcgi-pm-perl* libclass-accessor-perl* libclone-perl* libcroco3* libdigest-hmac-perl* libelf1* libemail-valid-perl* libexporter-tiny-perl* libfile-basedir-perl* libfile-stripnondeterminism-perl* libfuture-perl* libgcc-8-dev:armhf* libgcc1:armhf* libglib2.0-0* libgomp1:armhf* libio-async-perl* libio-pty-perl* libipc-run-perl* libipc-system-simple-perl* liblist-moreutils-perl* libncurses6* libnet-dns-perl* libnet-domain-tld-perl* libnet-ip-perl* libparse-debianchangelog-perl* libpath-tiny-perl* libpipeline1* libsigsegv2* libstdc++-8-dev:armhf* libstdc++6:armhf* libstruct-dumb-perl* libsub-name-perl* libtext-levenshtein-perl* libtool* libubsan1:armhf* libuchardet0* lintian* linux-libc-dev:armhf* m4* man-db* patchutils* po-debconf* sbuild-build-depends-lintian-dummy:armhf* sbuild-build-depends-main-dummy:armhf* t1utils* 0 upgraded, 0 newly installed, 69 to remove and 0 not upgraded. After this operation, 89.0 MB disk space will be freed. (Reading database ... 20512 files and directories currently installed.) Removing sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Removing sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Removing lintian (2.9.1) ... Removing diffstat (1.62-1) ... Removing libstdc++-8-dev:armhf (8.3.0-2) ... Removing libgcc-8-dev:armhf (8.3.0-2) ... Removing libubsan1:armhf (8.3.0-2) ... Removing libasan5:armhf (8.3.0-2) ... Removing libstdc++6:armhf (8.3.0-2) ... Removing help2man (1.47.8) ... Removing libapt-pkg-perl (0.1.34+b1) ... Removing libatomic1:armhf (8.3.0-2) ... Removing libc6-dev:armhf (2.28-8) ... Removing libgomp1:armhf (8.3.0-2) ... Removing libcapture-tiny-perl (0.48-1) ... Removing libparse-debianchangelog-perl (1.2.0-13) ... Removing libcgi-pm-perl (4.40-1) ... Removing libclass-accessor-perl (0.51-1) ... Removing libclone-perl (0.41-1+b1) ... Removing libemail-valid-perl (1.202-1) ... Removing libnet-dns-perl (1.19-1) ... Removing libdigest-hmac-perl (1.03+dfsg-2) ... Removing liblist-moreutils-perl (0.416-1+b4) ... Removing libexporter-tiny-perl (1.002001-1) ... Removing libfile-basedir-perl (0.08-1) ... Removing libio-async-perl (0.72-1) ... Removing libfuture-perl (0.39-1) ... Removing libipc-run-perl (20180523.0-1) ... Removing libio-pty-perl (1:1.08-1.1+b5) ... Removing libipc-system-simple-perl (1.25-4) ... Removing libnet-domain-tld-perl (1.75-1) ... Removing libnet-ip-perl (1.26-2) ... Removing libpath-tiny-perl (0.108-1) ... Removing libstruct-dumb-perl (0.09-1) ... Removing libsub-name-perl (0.21-1+b3) ... Removing libtext-levenshtein-perl (0.13-1) ... Removing linux-libc-dev:armhf (4.19.20-1) ... Removing patchutils (0.3.4-2) ... Removing t1utils (1.41-3) ... Removing libgcc1:armhf (1:8.3.0-2) ... Removing debhelper (12.1.1) ... Removing dh-strip-nondeterminism (1.1.1-1) ... Removing man-db (2.8.5-2) ... Removing bsdmainutils (11.1.2+b1) ... Removing dwz (0.12-3) ... Removing gcc-8-base:armhf (8.3.0-2) ... Removing po-debconf (1.0.21) ... Removing intltool-debian (0.35.0+20060710.5) ... Removing gettext (0.19.8.1-9) ... Removing gettext-base (0.19.8.1-9) ... Removing groff-base (1.22.4-3) ... Removing libfile-stripnondeterminism-perl (1.1.1-1) ... Removing libarchive-zip-perl (1.64-1) ... Removing libbsd0:amd64 (0.9.1-2) ... Removing libc6:armhf (2.28-8) ... Removing libcroco3:amd64 (0.6.12-3) ... Removing libelf1:amd64 (0.176-1) ... Removing libglib2.0-0:amd64 (2.58.3-1) ... Removing libncurses6:amd64 (6.1+20181013-2) ... Removing libpipeline1:amd64 (1.5.1-2) ... Removing libuchardet0:amd64 (0.0.6-3) ... Removing dh-autoreconf (19) ... Removing automake (1:1.16.1-4) ... Removing autoconf (2.69-11) ... Removing autopoint (0.19.8.1-9) ... Removing libtool (2.4.6-10) ... Removing autotools-dev (20180224.1) ... Removing m4 (1.4.18-2) ... Removing libsigsegv2:amd64 (2.12-2) ... Processing triggers for ccache (3.6-1) ... Updating symlinks in /usr/lib/ccache ... Processing triggers for libc-bin (2.28-8) ... (Reading database ... 16470 files and directories currently installed.) Purging configuration files for libglib2.0-0:amd64 (2.58.3-1) ... Purging configuration files for lintian (2.9.1) ... Purging configuration files for man-db (2.8.5-2) ... Purging configuration files for bsdmainutils (11.1.2+b1) ... Purging configuration files for autoconf (2.69-11) ... Purging configuration files for libc6:armhf (2.28-8) ... Purging configuration files for groff-base (1.22.4-3) ... +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 13 Distribution: unstable-amd64-sbuild Foreign Architectures: armhf Host Architecture: armhf Install-Time: 7 Job: /home/build/sbuild-setup/repo/pool/main/p/probalign/probalign_1.4-8.dsc Lintian: pass Machine Architecture: amd64 Package: probalign Package-Time: 24 Source-Version: 1.4-8 Space: n/a Status: successful Version: 1.4-8 -------------------------------------------------------------------------------- Finished at 2019-03-07T21:52:36Z Build needed 00:00:24, no disk space