sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | mafft 7.407-2 (mips64el) Tue, 18 Jun 2019 18:46:16 +0000 | +==============================================================================+ Package: mafft Version: 7.407-2 Source Version: 7.407-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: mips64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-eed8e995-866d-47e5-885d-3398d514ae0a' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [210 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-18-0818.52.pdiff [990 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-18-1419.13.pdiff [15.7 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-06-18-1419.13.pdiff [15.7 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-18-0818.52.pdiff [290 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-18-1419.13.pdiff [6341 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-06-18-1419.13.pdiff [6341 B] Get:8 http://debian.oregonstate.edu/debian unstable/main mips64el Packages [8016 kB] Fetched 8305 kB in 2s (4315 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'mafft' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mafft.git Please use: git clone https://salsa.debian.org/med-team/mafft.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 602 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main mafft 7.407-2 (dsc) [1963 B] Get:2 http://debian.oregonstate.edu/debian unstable/main mafft 7.407-2 (tar) [593 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main mafft 7.407-2 (diff) [6876 B] Fetched 602 kB in 0s (32.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/mafft-4UGykI/mafft-7.407' with '<>' I: NOTICE: Log filtering will replace 'build/mafft-4UGykI' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-mips64el:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Kc1HOg/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kc1HOg/apt_archive ./ Sources [364 B] Get:5 copy:/<>/resolver-Kc1HOg/apt_archive ./ Packages [454 B] Fetched 1775 B in 0s (97.2 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch g++-8-multilib-mips64el-linux-gnuabi64 gcc-8-doc libstdc++6-8-dbg-mips64el-cross gcc-8-multilib-mips64el-linux-gnuabi64 libgcc1-dbg-mips64el-cross libgomp1-dbg-mips64el-cross libitm1-dbg-mips64el-cross libatomic1-dbg-mips64el-cross libasan5-dbg-mips64el-cross liblsan0-dbg-mips64el-cross libtsan0-dbg-mips64el-cross libubsan1-dbg-mips64el-cross libmpx2-dbg-mips64el-cross libquadmath0-dbg-mips64el-cross manpages-dev autoconf automake libtool flex bison gdb-mips64el-linux-gnuabi64 gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-mips64el-linux-gnuabi64 cpp-8-mips64el-linux-gnuabi64 cpp-mips64el-linux-gnuabi64 cross-config crossbuild-essential-mips64el dpkg-cross file g++-8-mips64el-linux-gnuabi64 g++-mips64el-linux-gnuabi64 gcc-8-cross-base gcc-8-mips64el-linux-gnuabi64 gcc-8-mips64el-linux-gnuabi64-base gcc-mips64el-linux-gnuabi64 libatomic1-mips64el-cross libc6-dev-mips64el-cross libc6-mips64el-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-mips64el-cross libgcc1-mips64el-cross libgomp1-mips64el-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-mips64el-cross libstdc++6-mips64el-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-mips64el-cross sbuild-build-depends-core-dummy:mips64el sensible-utils ucf 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 40.4 MB of archives. After this operation, 151 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.35-4 [242 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.35-4 [117 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.35-4 [66.3 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-mips64el-linux-gnuabi64 amd64 2.31.1-16 [2489 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64-base amd64 8.3.0-7cross1 [191 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6277 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-7cross1 [186 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-mips64el-cross all 2.28-10cross2 [1355 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-mips64el-cross all 1:8.3.0-7cross1 [68.8 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-mips64el-cross all 8.3.0-7cross1 [66.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-mips64el-cross all 8.3.0-7cross1 [7384 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-mips64el-cross all 8.3.0-7cross1 [235 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6691 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1472 B] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-mips64el-cross all 8.3.0-7cross1 [310 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-mips64el-cross all 4.19.28-2cross2 [1240 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-mips64el-cross all 2.28-10cross2 [2512 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-mips64el-cross all 8.3.0-7cross1 [1559 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-mips64el-linux-gnuabi64 amd64 8.3.0-7cross1 [6850 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 g++-mips64el-linux-gnuabi64 amd64 4:8.3.0-1 [1192 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.00+dfsg-1 [58.6 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.27-1 [66.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-mips64el all 12.6 [6584 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.4 MB in 1s (62.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11954 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4_amd64.deb ... Unpacking file (1:5.35-4) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.35-4) ... Setting up gcc-8-cross-base (8.3.0-7cross1) ... Setting up libmagic1:amd64 (1:5.35-4) ... Setting up libc6-mips64el-cross (2.28-10cross2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.35-4) ... Setting up libyaml-perl (1.27-1) ... Setting up binutils-mips64el-linux-gnuabi64 (2.31.1-16) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-3) ... Setting up gcc-8-mips64el-linux-gnuabi64-base:amd64 (8.3.0-7cross1) ... Setting up sensible-utils (0.0.12) ... Setting up linux-libc-dev-mips64el-cross (4.19.28-2cross2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libgomp1-mips64el-cross (8.3.0-7cross1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libatomic1-mips64el-cross (8.3.0-7cross1) ... Setting up libgcc1-mips64el-cross (1:8.3.0-7cross1) ... Setting up libc6-dev-mips64el-cross (2.28-10cross2) ... Setting up ucf (3.0038+nmu1) ... Setting up libstdc++6-mips64el-cross (8.3.0-7cross1) ... Setting up cpp-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libgcc-8-dev-mips64el-cross (8.3.0-7cross1) ... Setting up libxml-sax-perl (1.00+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-mips64el-cross (8.3.0-7cross1) ... Setting up gcc-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up g++-8-mips64el-linux-gnuabi64 (8.3.0-7cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up g++-mips64el-linux-gnuabi64 (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-mips64el (12.6) ... Setting up sbuild-build-depends-core-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (mips64el included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-Kc1HOg/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kc1HOg/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-Kc1HOg/apt_archive ./ Packages [572 B] Fetched 2019 B in 0s (109 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:mips64el 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 844 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [844 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 844 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:mips64el. (Reading database ... 15129 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:mips64el (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~) Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~) dpkg-deb: building package 'sbuild-build-depends-mafft-dummy' in '/<>/resolver-Kc1HOg/apt_archive/sbuild-build-depends-mafft-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-mafft-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kc1HOg/apt_archive ./ Sources [632 B] Get:5 copy:/<>/resolver-Kc1HOg/apt_archive ./ Packages [713 B] Fetched 2308 B in 0s (121 kB/s) Reading package lists... Reading package lists... Install mafft build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libbsd0 libc6:mips64el libc6-dev:mips64el libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libglib2.0-0 libgomp1:mips64el libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:mips64el libstdc++6:mips64el libtool libuchardet0 linux-libc-dev:mips64el 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:mips64el libc-l10n:mips64el locales:mips64el manpages-dev:mips64el libstdc++-8-doc:mips64el libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:mips64el 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:mips64el gettext gettext-base groff-base intltool-debian libarchive-zip-perl libatomic1:mips64el libbsd0 libc6:mips64el libc6-dev:mips64el libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:mips64el libgcc1:mips64el libglib2.0-0 libgomp1:mips64el libncurses6 libpipeline1 libsigsegv2 libstdc++-8-dev:mips64el libstdc++6:mips64el libtool libuchardet0 linux-libc-dev:mips64el m4 man-db po-debconf sbuild-build-depends-mafft-dummy:mips64el 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After this operation, 90.2 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ sbuild-build-depends-mafft-dummy 0.invalid.0 [876 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12-3 [78.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.58.3-2 [1259 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.1.1 [1016 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main mips64el gcc-8-base mips64el 8.3.0-7 [191 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc1 mips64el 1:8.3.0-7 [68.5 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main mips64el libc6 mips64el 2.28-10 [2562 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main mips64el libatomic1 mips64el 8.3.0-7 [7432 B] Get:33 http://debian.oregonstate.edu/debian unstable/main mips64el linux-libc-dev mips64el 4.19.37-3 [1178 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main mips64el libc6-dev mips64el 2.28-10 [2513 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main mips64el libgomp1 mips64el 8.3.0-7 [67.3 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main mips64el libgcc-8-dev mips64el 8.3.0-7 [234 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++6 mips64el 8.3.0-7 [348 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main mips64el libstdc++-8-dev mips64el 8.3.0-7 [1573 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.3 MB in 0s (55.4 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15129 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../09-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../10-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../11-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../12-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-10_all.deb ... Unpacking libtool (2.4.6-10) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-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 .../16-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 .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../18-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../20-libglib2.0-0_2.58.3-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../21-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../22-libncurses6_6.1+20181013-2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2) ... Selecting previously unselected package gettext. Preparing to unpack .../23-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../24-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 .../25-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../26-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package gcc-8-base:mips64el. Preparing to unpack .../27-gcc-8-base_8.3.0-7_mips64el.deb ... Unpacking gcc-8-base:mips64el (8.3.0-7) ... Selecting previously unselected package libgcc1:mips64el. Preparing to unpack .../28-libgcc1_1%3a8.3.0-7_mips64el.deb ... Unpacking libgcc1:mips64el (1:8.3.0-7) ... Selecting previously unselected package libc6:mips64el. Preparing to unpack .../29-libc6_2.28-10_mips64el.deb ... Unpacking libc6:mips64el (2.28-10) ... Selecting previously unselected package libatomic1:mips64el. Preparing to unpack .../30-libatomic1_8.3.0-7_mips64el.deb ... Unpacking libatomic1:mips64el (8.3.0-7) ... Selecting previously unselected package linux-libc-dev:mips64el. Preparing to unpack .../31-linux-libc-dev_4.19.37-3_mips64el.deb ... Unpacking linux-libc-dev:mips64el (4.19.37-3) ... Selecting previously unselected package libc6-dev:mips64el. Preparing to unpack .../32-libc6-dev_2.28-10_mips64el.deb ... Unpacking libc6-dev:mips64el (2.28-10) ... Selecting previously unselected package libgomp1:mips64el. Preparing to unpack .../33-libgomp1_8.3.0-7_mips64el.deb ... Unpacking libgomp1:mips64el (8.3.0-7) ... Selecting previously unselected package libgcc-8-dev:mips64el. Preparing to unpack .../34-libgcc-8-dev_8.3.0-7_mips64el.deb ... Unpacking libgcc-8-dev:mips64el (8.3.0-7) ... Selecting previously unselected package libstdc++6:mips64el. Preparing to unpack .../35-libstdc++6_8.3.0-7_mips64el.deb ... Unpacking libstdc++6:mips64el (8.3.0-7) ... Selecting previously unselected package libstdc++-8-dev:mips64el. Preparing to unpack .../36-libstdc++-8-dev_8.3.0-7_mips64el.deb ... Unpacking libstdc++-8-dev:mips64el (8.3.0-7) ... Selecting previously unselected package sbuild-build-depends-mafft-dummy:mips64el. Preparing to unpack .../37-sbuild-build-depends-mafft-dummy_0.invalid.0_mips64el.deb ... Unpacking sbuild-build-depends-mafft-dummy:mips64el (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 (2.58.3-2) ... No schema files found: doing nothing. Setting up linux-libc-dev:mips64el (4.19.37-3) ... Setting up gettext-base (0.19.8.1-9) ... 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:mips64el (8.3.0-7) ... 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 (0.176-1.1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... 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:mips64el (2.28-10) ... Setting up libc6-dev:mips64el (2.28-10) ... Setting up libgcc1:mips64el (1:8.3.0-7) ... Setting up libgomp1:mips64el (8.3.0-7) ... Setting up dh-autoreconf (19) ... Setting up libatomic1:mips64el (8.3.0-7) ... Setting up libgcc-8-dev:mips64el (8.3.0-7) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up libstdc++6:mips64el (8.3.0-7) ... Setting up libstdc++-8-dev:mips64el (8.3.0-7) ... Setting up debhelper (12.1.1) ... Setting up sbuild-build-depends-mafft-dummy:mips64el (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.31.1-16 dpkg-dev_1.19.7 g++-8_8.3.0-7 gcc-8_8.3.0-7 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-mips64el-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-mips64el-cross_8.3.0-7cross1 linux-libc-dev_4.19.37-3 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16 binutils-common_2.31.1-16 binutils-mips64el-linux-gnuabi64_2.31.1-16 binutils-x86-64-linux-gnu_2.31.1-16 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_8.3.0-7 cpp-8-mips64el-linux-gnuabi64_8.3.0-7cross1 cpp-mips64el-linux-gnuabi64_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-mips64el_12.6 dash_0.5.10.2-5 debconf_1.5.72 debhelper_12.1.1 debian-archive-keyring_2019.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.45.2-1 fakeroot_1.23-1 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_8.3.0-7 g++-8-mips64el-linux-gnuabi64_8.3.0-7cross1 g++-mips64el-linux-gnuabi64_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-7 gcc-8-base_8.3.0-7 gcc-8-cross-base_8.3.0-7cross1 gcc-8-mips64el-linux-gnuabi64_8.3.0-7cross1 gcc-8-mips64el-linux-gnuabi64-base_8.3.0-7cross1 gcc-mips64el-linux-gnuabi64_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.13-2 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-7 libatomic1_8.3.0-7 libatomic1-mips64el-cross_8.3.0-7cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16 libblkid1_2.33.1-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-dev_2.28-10 libc6-dev-mips64el-cross_2.28-10cross2 libc6-mips64el-cross_2.28-10cross2 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-7 libcom-err2_1.45.2-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.2-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.1.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-7 libgcc-8-dev-mips64el-cross_8.3.0-7cross1 libgcc1_1:8.3.0-7 libgcc1-mips64el-cross_1:8.3.0-7cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-7 libgomp1-mips64el-cross_8.3.0-7cross1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.0.5-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_8.3.0-7 liblocale-gettext-perl_1.07-3+b4 liblsan0_8.3.0-7 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_8.3.0-7 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 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_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_8.3.0-7 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libss2_1.45.2-1 libstdc++-8-dev_8.3.0-7 libstdc++-8-dev-mips64el-cross_8.3.0-7cross1 libstdc++6_8.3.0-7 libstdc++6-mips64el-cross_8.3.0-7cross1 libsystemd0_241-5 libtasn1-6_4.13-3 libtinfo6_6.1+20181013-2 libtool_2.4.6-10 libtsan0_8.3.0-7 libubsan1_8.3.0-7 libuchardet0_0.0.6-3 libudev1_241-5 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.00+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.27-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-3 linux-libc-dev-mips64el-cross_4.19.28-2cross2 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 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-mafft-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Dec 2 10:43:32 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 ./mafft_7.407-2.dsc dpkg-source: info: extracting mafft in /<> dpkg-source: info: unpacking mafft_7.407.orig.tar.gz dpkg-source: info: unpacking mafft_7.407-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_bashism.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.mips64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-eed8e995-866d-47e5-885d-3398d514ae0a SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.407-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type mips64el-linux-gnuabi64 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 mips64el fakeroot debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j1 clean make[1]: Entering directory '/<>/core' rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno make[1]: Leaving directory '/<>/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/<>' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --sourcedirectory=core dh_update_autotools_config -a -O--sourcedirectory=core dh_autoreconf -a -O--sourcedirectory=core dh_auto_configure -a -O--sourcedirectory=core debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd core && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=mips64el-linux-gnuabi64-pkg-config CXX=mips64el-linux-gnuabi64-g\+\+ CC=mips64el-linux-gnuabi64-gcc PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from io.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ io.c: In function 'PreRead': io.c:1065:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); *locnjob = atoi( b ); ^~~~~~~~~~~~~~~~~~~ io.c:1070:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:1074:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); nleni = atoi( b ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'FRead': io.c:1110:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:1200:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_part_pointer': io.c:2635:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2636:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ^~~~~~~~~~~~~~~~~ io.c:2641:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_pointer': io.c:2671:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2672:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ^~~~~~~~~~~~~~~~~ io.c:2677:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf': io.c:2705:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2706:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2707:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_double': io.c:2735:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2736:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2737:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_int': io.c:2765:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2766:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2767:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_pointer': io.c:2796:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2797:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2798:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2': io.c:2826:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c:2827:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); ^~~~~~~~~~~~~~~~~ io.c:2828:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B, fp ); ^~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta_sub': io.c:3028:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3043:13: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadSsearch': io.c:3062:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_avscore': io.c:3190:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3197:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3198:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_scoreonly': io.c:3313:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3320:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3321:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7': io.c:3431:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3438:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3439:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34noalign': io.c:3463:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_nuc': io.c:3500:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3526:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10': io.c:3639:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3663:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nucbk': io.c:3766:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nuc': io.c:3816:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly': io.c:3877:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34': io.c:3933:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c:3959:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); // initn: ^~~~~~~~~~~~~~~~~~~ io.c:3962:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); // Smith-Waterman score ^~~~~~~~~~~~~~~~~~~ io.c:3974:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta3': io.c:3996:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta': io.c:4021:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt': io.c:4058:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt2': io.c:4079:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readOtherOptions': io.c:4175:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); ^~~~~~~~~~~~~~~~~~~ io.c: In function 'loadaamtx': io.c:5431:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( inorder, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5463:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5485:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, mf ); ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readsubalignmentstable': io.c:5631:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, linelen-1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5652:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, linelen-1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readmccaskill': io.c:5706:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5716:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readpairfoldalign': io.c:5775:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5788:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5795:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5809:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ io.c:5815:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from mltaln9.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mltaln9.c: In function 'check_guidetreefile': mltaln9.c:2802:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( string, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': mltaln9.c:15152:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &size, sizeof( int ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15153:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &opt, sizeof( double ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15156:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( m, size*sizeof( int ), 3, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15192:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &c, sizeof( char ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from mltaln9.c:1: In function 'fgets', inlined from 'check_guidetreefile' at mltaln9.c:2802:2: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from tddis.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from constants.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from constants.c:7: blosum.c: In function 'overridematrix': blosum.c:342:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( buf, 499, fp ); ^~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from nj.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from partSalignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Lalignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from rna.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ rna.c: In function 'rnaalifoldcall': rna.c:225:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( cmd ); ^~~~~~~~~~~~~ rna.c:245:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( cmd ); ^~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Salignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Dalignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Falign.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Falign_localhom.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Galign11.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from Lalign11.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from genalign11.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from MSalignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from fftFunctions.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from fft.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from tditeration.c:9: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from dvtditr.c:4: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ dvtditr.c: In function 'main': dvtditr.c:1020:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from defs.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from SAalignmm.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from treeOperation.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from addfunctions.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from dndfast7.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ dndfast7.c: In function 'main': dndfast7.c:328:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from dndblast.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ dndblast.c: In function 'main': dndblast.c:203:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ dndblast.c:384:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from sextet5.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from mafft-distance.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from MSalign11.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from suboptalign11.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from pairlocalalignmain.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from pairlocalalign.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1055:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1091:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:607:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calllast_fast': pairlocalalign.c:980:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'lastcallthread': pairlocalalign.c:871:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx_singleq': pairlocalalign.c:373:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readhat4': pairlocalalign.c:1531:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( oneline, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1543:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( oneline, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'recalllara': pairlocalalign.c:1244:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'callmxscarna_giving_bpp': pairlocalalign.c:1407:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1409:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1429:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1450:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1464:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1484:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1486:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calldafs_giving_bpp': pairlocalalign.c:1290:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1292:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairlocalalign.c:1312:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1333:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1343:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ pairlocalalign.c:1363:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1365:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1367:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'pairalign_node': pairlocalalign.c:3438:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "rm -rf hat3dir" ); // toriaezu ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3439:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "mkdir hat3dir" ); // toriaezu ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3444:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( fn ); ^~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from multi2hat3s.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ pairash.c: In function 'prepareash': pairash.c:639:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash': pairash.c:485:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairash.c: In function 'readrash': pairash.c:277:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'preparetmalign': pairash.c:530:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( linec, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign': pairash.c:347:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ pairash.c:356:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( com, 100, fp ); ^~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'readtmalign': pairash.c:228:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash.isra.1': pairash.c:428:29: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); ^ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:484:22: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); ^~ ~~~~~~~~~ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign.isra.2': pairash.c:346:27: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] sprintf( com, "mkdir -p %s", cachedir ); ^~ ~~~~~~~~ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:349:31: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); ^ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'preparetmalign.constprop': pairash.c:586:29: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf( command, "cp %s %s.pdb", sline, fname ); ^~ ~~~~~ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 9 or more bytes (assuming 1008) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:588:44: warning: '%s' directive writing up to 999 bytes into a region of size 983 [-Wformat-overflow=] sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname ); ^~ ~~~~~ In file included from /usr/mips64el-linux-gnuabi64/include/stdio.h:873, from mltaln.h:13, from pairash.c:1: /usr/mips64el-linux-gnuabi64/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 22 or more bytes (assuming 1021) into a destination of size 1000 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from addsingle.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread maffttext2hex.c: In function 'main': maffttext2hex.c:55:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( (char *)buf, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from splittbfast.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ splittbfast.c: In function 'main': splittbfast.c:3218:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from disttbfast.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ disttbfast.c: In function 'disttbfast': disttbfast.c:3638:6: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from tbfast.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ tbfast.c: In function 'main': tbfast.c:3181:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "cp infile.tree GuideTree" ); // tekitou ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from nodepair.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from mafft-profile.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from f2cl.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ f2cl.c: In function 'main': f2cl.c:283:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, B-1, orderfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from mccaskillwrap.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'athread': mccaskillwrap.c:115:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c:117:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c:129:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); // for cygwin, wakaran ^~~~~~~~~~~~~ mccaskillwrap.c:155:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); ^~~~~~~~~~~~~ mccaskillwrap.c: In function 'readrawmccaskill': mccaskillwrap.c:46:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from contrafoldwrap.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ contrafoldwrap.c: In function 'readcontrafold': contrafoldwrap.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); ^~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from countlen.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from seq2regtable.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from regtable2seq.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ regtable2seq.c: In function 'readereg': regtable2seq.c:69:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c: In function 'readreg': regtable2seq.c:120:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, regfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from score.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from getlag.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from dndpre.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from setcore.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from replaceu.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from restoreu.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ restoreu.c: In function 'main': restoreu.c:177:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, dlfp ); ^~~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from setdirection.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ setdirection.c: In function 'main': setdirection.c:132:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 99, difp ); ^~~~~~~~~~~~~~~~~~~~~~~ mips64el-linux-gnuabi64-gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from makedirectionlist.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ mips64el-linux-gnuabi64-gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread mips64el-linux-gnuabi64-gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread In file included from /usr/mips64el-linux-gnuabi64/include/bits/libc-header-start.h:33, from /usr/mips64el-linux-gnuabi64/include/stdio.h:27, from mltaln.h:13, from version.c:1: /usr/mips64el-linux-gnuabi64/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory '/<>/core' make[1]: Leaving directory '/<>' dh_auto_test -a -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --sourcedirectory=core dh_testroot -a -O--sourcedirectory=core dh_prep -a -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft cd core && make -j1 install DESTDIR=/<>/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory '/<>/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /<>/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /<>/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /<>/debian/mafft/usr/lib/mafft/bin chmod 755 /<>/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /<>/debian/mafft/usr/lib/mafft/bin install: WARNING: ignoring --strip-program option as -s option was not specified chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails install --strip-program=true -s dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore replaceu restoreu setdirection makedirectionlist version /<>/debian/mafft/usr/lib/mafft/lib/mafft install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /<>/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /<>/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /<>/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /<>/debian/mafft/usr/share/man/man1 chmod 755 /<>/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /<>/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/<>/core' rm debian/mafft/usr/lib/mafft/lib/mafft/*.1 make[1]: Leaving directory '/<>' dh_installdocs -a -O--sourcedirectory=core dh_installchangelogs -a -O--sourcedirectory=core dh_installman -a -O--sourcedirectory=core dh_installinit -a -O--sourcedirectory=core dh_perl -a -O--sourcedirectory=core dh_link -a -O--sourcedirectory=core dh_strip_nondeterminism -a -O--sourcedirectory=core debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -X test/sample make[1]: Leaving directory '/<>' dh_fixperms -a -O--sourcedirectory=core dh_missing -a -O--sourcedirectory=core dh_strip -a -O--sourcedirectory=core dh_makeshlibs -a -O--sourcedirectory=core dh_shlibdeps -a -O--sourcedirectory=core dh_installdeb -a -O--sourcedirectory=core dh_gencontrol -a -O--sourcedirectory=core dh_md5sums -a -O--sourcedirectory=core dh_builddeb -a -O--sourcedirectory=core dpkg-deb: building package 'mafft' in '../mafft_7.407-2_mips64el.deb'. dpkg-deb: building package 'mafft-dbgsym' in '../mafft-dbgsym_7.407-2_mips64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../mafft_7.407-2_mips64el.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 2019-06-18T18:48:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-Kc1HOg/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-mafft-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Kc1HOg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Kc1HOg/apt_archive ./ Sources [754 B] Get:5 copy:/<>/resolver-Kc1HOg/apt_archive ./ Packages [827 B] Fetched 2544 B in 0s (138 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 additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 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 libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libhtml-template-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 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 libhtml-parser-perl libhtml-tagset-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline7 libsqlite3-0 libssl1.1 libstruct-dumb-perl libsub-name-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:mips64el t1utils 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 7774 kB of archives. After this operation, 20.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Kc1HOg/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 7.0-5 [70.6 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.2-1 [49.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.13-2 [512 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.27.2-3 [641 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.13-2 [866 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.34+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.40-1 [222 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.85-2+b1 [308 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.19-1 [372 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.39-1 [74.5 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.72-1 [262 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.76+repack-1 [33.1 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2 [90.4 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.15.0 [1181 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7774 kB in 0s (36.9 MB/s) Selecting previously unselected package netbase. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mafft_7.407-2_mips64el.changes: ------------------------------- Format: 1.8 Date: Sun, 02 Dec 2018 11:39:45 +0100 Source: mafft Binary: mafft mafft-dbgsym Built-For-Profiles: cross nocheck Architecture: mips64el Version: 7.407-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Closes: 914715 Changes: mafft (7.407-2) unstable; urgency=medium . [ Helmut Grohne ] * Fix FTCBFS: Let dh_auto_build pass cross tools to make. (Closes: #914715) * Also simplify debian/rules using --sourcedirectory. . [ Andreas Tille ] * Remove trailing whitespace in debian/changelog Checksums-Sha1: 056e528a9e8301e81baf50dbc8adeef56cc020a2 10463616 mafft-dbgsym_7.407-2_mips64el.deb bb434ba64a8004366c28aae708af2eddf9e5abf0 4423 mafft_7.407-2_mips64el.buildinfo 832ce5e613bc2f1d91c74b71fec6b68f26728c31 831888 mafft_7.407-2_mips64el.deb Checksums-Sha256: 0c7ea8b337b27f460522cd87999624dee3b154fbf1ef3ee958bfc88c60199101 10463616 mafft-dbgsym_7.407-2_mips64el.deb 30f49c50be909ebcd21bc3a043868f2df503c2fc0dbf41ca480727d68aa93656 4423 mafft_7.407-2_mips64el.buildinfo fd691eabd012cd1189066fbc1c303a9fa3bbd2d0cd1e63de4fe575d08b9c9b59 831888 mafft_7.407-2_mips64el.deb Files: dfb042bab71bbf8bee72a4504d65214d 10463616 debug optional mafft-dbgsym_7.407-2_mips64el.deb 4c3733d68e647746bf43d61ccf2b3b23 4423 science optional mafft_7.407-2_mips64el.buildinfo 49c0daf1967c3187fc3d56c56baa1101 831888 science optional mafft_7.407-2_mips64el.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: mafft Binary: mafft Architecture: mips64el Version: 7.407-2 Checksums-Md5: dfb042bab71bbf8bee72a4504d65214d 10463616 mafft-dbgsym_7.407-2_mips64el.deb 49c0daf1967c3187fc3d56c56baa1101 831888 mafft_7.407-2_mips64el.deb Checksums-Sha1: 056e528a9e8301e81baf50dbc8adeef56cc020a2 10463616 mafft-dbgsym_7.407-2_mips64el.deb 832ce5e613bc2f1d91c74b71fec6b68f26728c31 831888 mafft_7.407-2_mips64el.deb Checksums-Sha256: 0c7ea8b337b27f460522cd87999624dee3b154fbf1ef3ee958bfc88c60199101 10463616 mafft-dbgsym_7.407-2_mips64el.deb fd691eabd012cd1189066fbc1c303a9fa3bbd2d0cd1e63de4fe575d08b9c9b59 831888 mafft_7.407-2_mips64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 18 Jun 2019 18:48:08 +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 (= 10.3), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.31.1-16), binutils-common (= 2.31.1-16), binutils-x86-64-linux-gnu (= 2.31.1-16), 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 (= 8.3.0-7), dash (= 0.5.10.2-5), debconf (= 1.5.72), debhelper (= 12.1.1), debianutils (= 4.8.6.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.1.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), 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 (= 8.3.0-7), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-7), gcc-8-base (= 8.3.0-7), 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), 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 (= 8.3.0-7), libatomic1 (= 8.3.0-7), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.4-3), libaudit1 (= 1:2.8.4-3), libbinutils (= 2.31.1-16), libblkid1 (= 2.33.1-0.1), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9), libc-bin (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 8.3.0-7), libcroco3 (= 0.6.12-3), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.33.1-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.1.2-1), libgcc-8-dev (= 8.3.0-7), libgcc1 (= 1:8.3.0-7), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4), libgdbm6 (= 1.18.1-4), libglib2.0-0 (= 2.58.3-2), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 8.3.0-7), libgpg-error0 (= 1.35-1), libicu63 (= 63.2-2), libisl19 (= 0.20-2), libitm1 (= 8.3.0-7), liblsan0 (= 8.3.0-7), 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 (= 8.3.0-7), 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 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libquadmath0 (= 8.3.0-7), libseccomp2 (= 2.3.3-4), libselinux1 (= 2.8-1+b1), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.33.1-0.1), libstdc++-8-dev (= 8.3.0-7), libstdc++6 (= 8.3.0-7), libsystemd0 (= 241-5), libtinfo6 (= 6.1+20181013-2), libtool (= 2.4.6-10), libtsan0 (= 8.3.0-7), libubsan1 (= 8.3.0-7), libuchardet0 (= 0.0.6-3), libudev1 (= 241-5), libunistring2 (= 0.9.10-1), libuuid1 (= 2.33.1-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 4.19.37-3), 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 (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.93-8), tar (= 1.30+dfsg-6), 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=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1543747185" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ mafft-dbgsym_7.407-2_mips64el.deb --------------------------------- new Debian package, version 2.0. size 10463616 bytes: control archive=1948 bytes. 1597 bytes, 12 lines control 3286 bytes, 31 lines md5sums Package: mafft-dbgsym Source: mafft Version: 7.407-2 Auto-Built-Package: debug-symbols Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 23705 Depends: mafft (= 7.407-2) Section: debug Priority: optional Description: debug symbols 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./usr/lib/debug/.build-id/eb/81736478e961e6383118c9f2e8050cc6fd6be0.debug drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 1233048 2018-12-02 10:39 ./usr/lib/debug/.build-id/f8/6a7942d53c4534b9837f31c291a4d66e8966d7.debug drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/debug/.build-id/f9/ -rw-r--r-- root/root 677336 2018-12-02 10:39 ./usr/lib/debug/.build-id/f9/fa41a8dd21b1407a96f1f9d423f02d8798bc0c.debug drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/doc/ lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/doc/mafft-dbgsym -> mafft mafft_7.407-2_mips64el.deb -------------------------- new Debian package, version 2.0. size 831888 bytes: control archive=2344 bytes. 1388 bytes, 30 lines control 3783 bytes, 54 lines md5sums Package: mafft Version: 7.407-2 Architecture: mips64el Maintainer: Debian Med Packaging Team Installed-Size: 12090 Depends: libc6 (>= 2.7), perl:any Recommends: blast2, libwww-perl, lynx, ruby Enhances: t-coffee Section: science Priority: optional Homepage: http://mafft.cbrc.jp/alignment/software/ Description: Multiple alignment program for amino acid or nucleotide sequences MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm). drwxr-xr-x root/root 0 2018-12-02 10:39 ./ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/bin/ lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/bin/mafft -> ../lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/bin/mafft-profile -> ../lib/mafft/bin/mafft-profile drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/mafft/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/ lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/einsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/fftns -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/fftnsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/ginsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/linsi -> mafft -rwxr-xr-x root/root 101030 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-einsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-fftns -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-ginsi -> mafft -rwxr-xr-x root/root 8958 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-linsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-nwns -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-qinsi -> mafft -rwxr-xr-x root/root 7785 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-sparsecore.rb lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/mafft-xinsi -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/nwns -> mafft lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/lib/mafft/bin/nwnsi -> mafft drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/mafft/lib/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/ -rwxr-xr-x root/root 617328 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/addsingle -rwxr-xr-x root/root 336344 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/contrafoldwrap -rwxr-xr-x root/root 104008 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/countlen -rwxr-xr-x root/root 625616 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/disttbfast -rwxr-xr-x root/root 349832 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/dndblast -rwxr-xr-x root/root 349832 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/dndfast7 -rwxr-xr-x root/root 336320 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/dndpre -rwxr-xr-x root/root 630400 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/dvtditr -rwxr-xr-x root/root 170320 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/f2cl -rwxr-xr-x root/root 562536 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/getlag -rwxr-xr-x root/root 10896 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/hex2maffttext -rwxr-xr-x root/root 349960 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/mafft-distance -rwxr-xr-x root/root 562496 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/mafft-profile -rwxr-xr-x root/root 10475 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/mafftash_premafft.pl -rwxr-xr-x root/root 10904 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/maffttext2hex -rwxr-xr-x root/root 588008 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/makedirectionlist -rwxr-xr-x root/root 340480 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/mccaskillwrap -rwxr-xr-x root/root 362808 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/multi2hat3s -rwxr-xr-x root/root 629552 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/nodepair -rwxr-xr-x root/root 575168 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/pairash -rwxr-xr-x root/root 604192 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/pairlocalalign -rwxr-xr-x root/root 278432 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/regtable2seq -rwxr-xr-x root/root 274288 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/replaceu -rwxr-xr-x root/root 278368 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/restoreu -rwxr-xr-x root/root 332136 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/score -rwxr-xr-x root/root 15541 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/seekquencer_premafft.pl -rwxr-xr-x root/root 108120 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/seq2regtable -rwxr-xr-x root/root 562472 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/setcore -rwxr-xr-x root/root 278376 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/setdirection -rwxr-xr-x root/root 349920 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/sextet5 -rwxr-xr-x root/root 587632 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/splittbfast -rwxr-xr-x root/root 675272 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/tbfast -rwxr-xr-x root/root 6712 2018-12-02 10:39 ./usr/lib/mafft/lib/mafft/version drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/doc/mafft/ -rw-r--r-- root/root 3573 2018-12-02 10:39 ./usr/share/doc/mafft/changelog.Debian.gz -rw-r--r-- root/root 1931 2018-12-02 10:39 ./usr/share/doc/mafft/copyright drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/doc/mafft/test/ -rw-r--r-- root/root 16616 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample -rw-r--r-- root/root 29932 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.dpparttree -rw-r--r-- root/root 29176 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.fftns2 -rw-r--r-- root/root 29068 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.fftnsi -rw-r--r-- root/root 29896 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.gins1 -rw-r--r-- root/root 29356 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.ginsi -rw-r--r-- root/root 42640 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.ginsi.allowshift -rw-r--r-- root/root 28888 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.lins1 -rw-r--r-- root/root 29824 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.linsi -rw-r--r-- root/root 29932 2018-08-06 03:30 ./usr/share/doc/mafft/test/sample.parttree -rw-r--r-- root/root 1502 2018-08-06 03:30 ./usr/share/doc/mafft/test/samplerna -rw-r--r-- root/root 1916 2018-08-06 03:30 ./usr/share/doc/mafft/test/samplerna.qinsi -rw-r--r-- root/root 1916 2018-08-06 03:30 ./usr/share/doc/mafft/test/samplerna.xinsi -rw-r--r-- root/root 725 2018-08-06 03:30 ./usr/share/doc/mafft/test/script drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/man/ drwxr-xr-x root/root 0 2018-12-02 10:39 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz -rw-r--r-- root/root 2130 2018-12-02 10:39 ./usr/share/man/man1/mafft-homologs.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2018-12-02 10:39 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz -rw-r--r-- root/root 4421 2018-12-02 10:39 ./usr/share/man/man1/mafft.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 159800 Build-Time: 78 Distribution: unstable Foreign Architectures: mips64el Host Architecture: mips64el Install-Time: 25 Job: mafft_7.407-2 Lintian: pass Machine Architecture: amd64 Package: mafft Package-Time: 113 Source-Version: 7.407-2 Space: 159800 Status: successful Version: 7.407-2 -------------------------------------------------------------------------------- Finished at 2019-06-18T18:48:09Z Build needed 00:01:53, 159800k disk space