sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | mafft 7.429-1 (armhf) Wed, 18 Sep 2019 01:03:14 +0000 | +==============================================================================+ Package: mafft Version: 7.429-1 Source Version: 7.429-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-956dd265-1165-44ff-b6f0-a07c52c9bb2e' with '<>' I: NOTICE: Log filtering will replace 'build/mafft-WHpVxD/resolver-vUMweR' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 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 2019-09-17-0811.06.pdiff [6662 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-17-1412.34.pdiff [9806 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-17-2019.22.pdiff [7028 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-17-2019.22.pdiff [7028 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-17-0811.06.pdiff [7149 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-17-1412.34.pdiff [8714 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-17-2019.22.pdiff [16.0 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armhf Packages [7998 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-17-2019.22.pdiff [16.0 kB] Fetched 8248 kB in 2s (4205 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 613 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main mafft 7.429-1 (dsc) [1972 B] Get:2 http://debian.oregonstate.edu/debian unstable/main mafft 7.429-1 (tar) [605 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main mafft 7.429-1 (diff) [6588 B] Fetched 613 kB in 0s (57.8 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/mafft-WHpVxD/mafft-7.429' with '<>' I: NOTICE: Log filtering will replace 'build/mafft-WHpVxD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [404 B] Get:5 copy:/<>/apt_archive ./ Packages [492 B] Fetched 1853 B in 0s (110 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf libstdc++-9-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdmainutils cpp-9-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf gcc-9-arm-linux-gnueabihf-base gcc-9-base:armhf gcc-9-cross-base gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan5-armhf-cross libatomic1:armhf libatomic1-armhf-cross libbsd0 libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armhf libgcc-9-dev-armhf-cross libgcc1:armhf libgcc1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libpipeline1 libsigsegv2 libstdc++-9-dev:armhf libstdc++-9-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils ucf 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 61.9 MB of archives. After this operation, 238 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 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 2.8.7-3 [1300 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.2.1-8 [193 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.32.51.20190909-1 [2719 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf-base amd64 9.2.1-8cross1 [193 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [6808 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [16.7 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-8cross1 [188 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.29-1cross7 [1122 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:9.2.1-8cross1 [37.3 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 9.2.1-8cross1 [73.3 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 9.2.1-8cross1 [6688 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 9.2.1-8cross1 [362 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 9.2.1-8cross1 [392 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 9.2.1-8cross1 [112 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armhf-cross all 9.2.1-8cross1 [665 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [7143 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1476 B] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 5.2.9-2cross7 [1312 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.29-1cross7 [2122 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armhf-cross all 9.2.1-8cross1 [1717 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabihf amd64 9.2.1-8cross1 [7385 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:9.2.1-3.1 [1184 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.8 [6644 B] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.65-1 [95.8 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.0-1 [23.3 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.0-1 [14.3 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-1 [81.8 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.6.1 [172 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.60.6-2 [1295 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190803-1 [102 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.6.1 [993 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:9.2.1-8 [37.3 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.29-1 [2339 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.2.1-8 [370 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 9.2.1-8 [6868 B] Get:79 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.2.9-2 [1216 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.29-1 [2142 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 9.2.1-8 [75.3 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 9.2.1-8 [431 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 9.2.1-8 [113 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-9-dev armhf 9.2.1-8 [665 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-9-dev armhf 9.2.1-8 [1748 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.9 MB in 1s (66.7 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 13083 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... 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_2.8.7-3_amd64.deb ... Unpacking man-db (2.8.7-3) ... 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Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.29-1cross7) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.65-1) ... Setting up libglib2.0-0:amd64 (2.60.6-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.6.1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up linux-libc-dev:armhf (5.2.9-2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up gcc-9-arm-linux-gnueabihf-base:amd64 (9.2.1-8cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20190803-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up linux-libc-dev-armhf-cross (5.2.9-2cross7) ... Setting up autopoint (0.19.8.1-9) ... Setting up gcc-9-cross-base (9.2.1-8cross1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up binutils-arm-linux-gnueabihf (2.32.51.20190909-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up gcc-9-base:armhf (9.2.1-8) ... Setting up libgomp1-armhf-cross (9.2.1-8cross1) ... Setting up libfile-stripnondeterminism-perl (1.6.0-1) ... Setting up libtool (2.4.6-11) ... Setting up cpp-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libc6-dev-armhf-cross (2.29-1cross7) ... Setting up m4 (1.4.18-2) ... Setting up libatomic1-armhf-cross (9.2.1-8cross1) ... Setting up libgcc1-armhf-cross (1:9.2.1-8cross1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up cpp-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+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 libasan5-armhf-cross (9.2.1-8cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libstdc++6-armhf-cross (9.2.1-8cross1) ... Setting up libubsan1-armhf-cross (9.2.1-8cross1) ... 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 libgcc-9-dev-armhf-cross (9.2.1-8cross1) ... Setting up po-debconf (1.0.21) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libstdc++-9-dev-armhf-cross (9.2.1-8cross1) ... Setting up gcc-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-9-arm-linux-gnueabihf (9.2.1-8cross1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up g++-arm-linux-gnueabihf (4:9.2.1-3.1) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.8) ... Setting up libgcc1:armhf (1:9.2.1-8) ... Setting up dh-autoreconf (19) ... Setting up libc6:armhf (2.29-1) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up libc6-dev:armhf (2.29-1) ... Setting up libstdc++6:armhf (9.2.1-8) ... Setting up debhelper (12.6.1) ... Setting up libgomp1:armhf (9.2.1-8) ... Setting up libasan5:armhf (9.2.1-8) ... Setting up libatomic1:armhf (9.2.1-8) ... Setting up libubsan1:armhf (9.2.1-8) ... Setting up libgcc-9-dev:armhf (9.2.1-8) ... Setting up libstdc++-9-dev:armhf (9.2.1-8) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.29-1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190909-1 dpkg-dev_1.19.7 g++-8_8.3.0-22 g++-9_9.2.1-8 gcc-8_8.3.0-22 gcc-9_9.2.1-8 libc6-dev_2.29-1 libstdc++-8-dev_8.3.0-22 libstdc++-9-dev_9.2.1-8 libstdc++-9-dev-armhf-cross_9.2.1-8cross1 libstdc++6_9.2.1-8 libstdc++6-armhf-cross_9.2.1-8cross1 linux-libc-dev_5.2.9-2 Package versions: adduser_3.118 apt_1.8.3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190909-1 binutils-arm-linux-gnueabihf_2.32.51.20190909-1 binutils-common_2.32.51.20190909-1 binutils-x86-64-linux-gnu_2.32.51.20190909-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-22 cpp-9_9.2.1-8 cpp-9-arm-linux-gnueabihf_9.2.1-8cross1 cpp-arm-linux-gnueabihf_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.6.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.3-4 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-22 g++-9_9.2.1-8 g++-9-arm-linux-gnueabihf_9.2.1-8cross1 g++-arm-linux-gnueabihf_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-22 gcc-8-base_8.3.0-22 gcc-9_9.2.1-8 gcc-9-arm-linux-gnueabihf_9.2.1-8cross1 gcc-9-arm-linux-gnueabihf-base_9.2.1-8cross1 gcc-9-base_9.2.1-8 gcc-9-cross-base_9.2.1-8cross1 gcc-arm-linux-gnueabihf_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.22+b1 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.3 libarchive-zip-perl_1.65-1 libasan5_9.2.1-8 libasan5-armhf-cross_9.2.1-8cross1 libatomic1_9.2.1-8 libatomic1-armhf-cross_9.2.1-8cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190909-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-1 libc-dev-bin_2.29-1 libc6_2.29-1 libc6-armhf-cross_2.29-1cross7 libc6-dev_2.29-1 libc6-dev-armhf-cross_2.29-1cross7 libcap-ng0_0.7.9-2+b1 libcc1-0_9.2.1-8 libcom-err2_1.45.3-4 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.6.1 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libyaml-perl_1.29-1 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.2.9-2 linux-libc-dev-armhf-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.3-4 lsb-base_11.1.0 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 passwd_1:4.7-2 patch_2.7.6-6 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-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96~beta-1 tar_1.30+dfsg-6+b1 tzdata_2019c-1 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: mafft Binary: mafft Architecture: any Version: 7.429-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://mafft.cbrc.jp/alignment/software/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/mafft Vcs-Git: https://salsa.debian.org/med-team/mafft.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12) Package-List: mafft deb science optional arch=any Checksums-Sha1: c7e50bb1ff43140ce7d67691a0a4c2c82981542a 604929 mafft_7.429.orig.tar.gz a8cf6f20b60e5d9226af8f063dd092cc07fafdbb 6588 mafft_7.429-1.debian.tar.xz Checksums-Sha256: 6e22e0d6130862c67233ab3a13a70febf7f5a1e0a8ab0d73420ca70496b167bc 604929 mafft_7.429.orig.tar.gz d0d63d2fc2a7e812e7d59bf7a9f482eab8ef48923e71e451f9405fd048f09920 6588 mafft_7.429-1.debian.tar.xz Files: 5a561c68604fc9b63001eeb0d6966912 604929 mafft_7.429.orig.tar.gz f82cebc8ecdb3887125c799a1f845935 6588 mafft_7.429-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl08MCMTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0ej0D/47f67I/1SjnaaYGbKl9y4a1YZ6HETL 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signature: No public key dpkg-source: warning: failed to verify signature on ./mafft_7.429-1.dsc dpkg-source: info: extracting mafft in /<> dpkg-source: info: unpacking mafft_7.429.orig.tar.gz dpkg-source: info: unpacking mafft_7.429-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 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-956dd265-1165-44ff-b6f0-a07c52c9bb2e SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.429-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --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=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-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 arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from io.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 1065 | 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] 1070 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1074:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1074 | 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] 1110 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1200:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1200 | 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] 2635 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2636:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2636 | 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] 2641 | 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] 2671 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2672:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2672 | 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] 2677 | 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] 2705 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2706:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2706 | 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] 2707 | 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] 2735 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2736:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2736 | 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] 2737 | 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] 2765 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2766:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2766 | 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] 2767 | 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] 2796 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2797:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2797 | 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] 2798 | 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] 2826 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2827:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | 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] 2828 | 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] 3028 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3043:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3043 | 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] 3062 | 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] 3190 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3197:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3197 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3198:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3198 | 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] 3313 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3320:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3320 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3321:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3321 | 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] 3431 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3438:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3438 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3439:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3439 | 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] 3463 | 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] 3500 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3526:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3526 | 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] 3639 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3663:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3663 | 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] 3766 | 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] 3816 | 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] 3877 | 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] 3933 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3959:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3959 | fgets( b, B-1, fp ); // initn: | ^~~~~~~~~~~~~~~~~~~ io.c:3962:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3962 | 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] 3974 | 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] 3996 | 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] 4021 | 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] 4058 | 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] 4079 | 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] 4175 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘loadaamtx’: io.c:5433:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5433 | fgets( inorder, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5465:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5465 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5488:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5488 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readsubalignmentstable’: io.c:5644:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5644 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5665:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5665 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readmccaskill’: io.c:5719:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5719 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5729:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5729 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readpairfoldalign’: io.c:5788:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5788 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5801:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5801 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5808:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5808 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5822:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5822 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5828:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5828 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from mltaln9.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 2802 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘readlocalhomtable2_single_bin_noseek’: mltaln9.c:15112:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15112 | fread( &size, sizeof( int ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15113:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15113 | fread( &opt, sizeof( double ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15116:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15116 | fread( m, size*sizeof( int ), 3, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15152:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 15152 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘createchain’: mltaln9.c:2065:17: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2065 | instanttree = calloc( treelen, sizeof( char ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:14, from mltaln9.c:1: /usr/arm-linux-gnueabihf/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here 541 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ mltaln9.c:2076:10: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 2076 | order = calloc( nseq, sizeof( int ) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:14, from mltaln9.c:1: /usr/arm-linux-gnueabihf/include/stdlib.h:541:14: note: in a call to allocation function ‘calloc’ declared here 541 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from mltaln9.c:1: In function ‘fgets’, inlined from ‘check_guidetreefile’ at mltaln9.c:2802:2: /usr/arm-linux-gnueabihf/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 [-Wattribute-warning] 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from tddis.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from constants.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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:369:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 369 | fgets( buf, 499, fp ); | ^~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from nj.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from partSalignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Lalignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from rna.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 225 | system( cmd ); | ^~~~~~~~~~~~~ rna.c:245:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 245 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Salignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Dalignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Falign.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Falign_localhom.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Galign11.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from Lalign11.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from genalign11.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from MSalignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from fftFunctions.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from fft.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from tditeration.c:9: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from dvtditr.c:4: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 1020 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from defs.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from SAalignmm.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from treeOperation.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from addfunctions.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from dndfast7.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dndfast7.c: In function ‘main’: dndfast7.c:326:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 326 | system( com ); | ^~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from dndblast.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ dndblast.c: In function ‘main’: dndblast.c:201:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 201 | system( com ); | ^~~~~~~~~~~~~ dndblast.c:382:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from sextet5.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from mafft-distance.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from MSalign11.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from suboptalign11.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from pairlocalalignmain.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from pairlocalalign.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 1055 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1091:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1091 | 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] 607 | 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] 980 | 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] 871 | 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] 373 | 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] 1531 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1543:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1543 | 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] 1244 | 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] 1407 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1409:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1409 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1429:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1429 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1450:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1450 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1464:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1464 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1484:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1484 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1486:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1486 | 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] 1290 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1292:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1292 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1312:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1312 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1333:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1333 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1343:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1343 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1363:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1363 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1365:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1365 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1367:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 1367 | 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] 3438 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3439:2: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3439 | system( "mkdir hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3444:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3444 | system( fn ); | ^~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from multi2hat3s.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 639 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 681 | 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] 485 | 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] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 289 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 294 | 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] 530 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 576 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 587 | 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] 321 | 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] 347 | system( com ); | ^~~~~~~~~~~~~ pairash.c:356:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 356 | 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] 228 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 232 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 235 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 238 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash.isra.0’: pairash.c:428:29: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); | ^ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 8 or more bytes (assuming 10007) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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=] 484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); | ^~ ~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 11014 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign.isra.0’: pairash.c:346:27: warning: ‘%s’ directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); | ^~ ~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 10 and 10009 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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=] 349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); | ^ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10002) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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=] 586 | sprintf( command, "cp %s %s.pdb", sline, fname ); | ^~ ~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 9 or more bytes (assuming 1008) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __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=] 588 | sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname ); | ^~ ~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:867, from mltaln.h:13, from pairash.c:1: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 22 or more bytes (assuming 1021) into a destination of size 1000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from addsingle.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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] 55 | fgets( (char *)buf, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from splittbfast.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 3218 | system( com ); | ^~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from disttbfast.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 3638 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from tbfast.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ tbfast.c: In function ‘main’: tbfast.c:3190:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 3190 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from nodepair.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from mafft-profile.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from f2cl.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ f2cl.c: In function ‘main’: f2cl.c:287:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 287 | fgets( gett, B-1, orderfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from mccaskillwrap.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 372 | 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] 115 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:117:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 117 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:129:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 129 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ mccaskillwrap.c:155:4: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 155 | 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] 46 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from contrafoldwrap.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from countlen.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from seq2regtable.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from regtable2seq.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 69 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 97 | 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] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from score.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from getlag.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from dndpre.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from setcore.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from replaceu.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from restoreu.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 177 | fgets( gett, 999, dlfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from setdirection.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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] 132 | fgets( line, 99, difp ); | ^~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from makedirectionlist.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" | ^~~~~~~ arm-linux-gnueabihf-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 arm-linux-gnueabihf-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/arm-linux-gnueabihf/include/bits/libc-header-start.h:33, from /usr/arm-linux-gnueabihf/include/stdio.h:27, from mltaln.h:13, from version.c:1: /usr/arm-linux-gnueabihf/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] 185 | # 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_installsystemduser -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_dwz -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_7.429-1_armhf.deb'. dpkg-deb: building package 'mafft-dbgsym' in '../mafft-dbgsym_7.429-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../mafft_7.429-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-09-18T01:04:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ mafft_7.429-1_armhf.changes: ---------------------------- Format: 1.8 Date: Sat, 27 Jul 2019 12:56:27 +0200 Source: mafft Binary: mafft mafft-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 7.429-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (7.429-1) unstable; urgency=medium . * Team upload. * New upstream version * debhelper-compat 12 * Created with routine-update script. * Standards-Version: 4.4.0 Checksums-Sha1: 3a01bbe1532e02be6546db85677fb69f6617d5d9 9017964 mafft-dbgsym_7.429-1_armhf.deb 7a58a877d4743a5f4e15b62a730d95593c2609f1 4645 mafft_7.429-1_armhf.buildinfo 6e60ff8e1d6f25d5b6af5c4dde9d2d18b1965187 737648 mafft_7.429-1_armhf.deb Checksums-Sha256: 5344a5289985ba00e77a81a6a9098d68bfe1de93defadc9332e9cde26f7d908e 9017964 mafft-dbgsym_7.429-1_armhf.deb e1c5a69406b1765f4444e31daa579368b9fae07c6c55726da8998f872837e3e8 4645 mafft_7.429-1_armhf.buildinfo 8628022fb947fc284700eb845dfbc9fec10777196fb2d94d19533ef6d4706fae 737648 mafft_7.429-1_armhf.deb Files: e1ca996338ec0860f32d63e6002c2add 9017964 debug optional mafft-dbgsym_7.429-1_armhf.deb 30e62eb68b8a493788658201a4462244 4645 science optional mafft_7.429-1_armhf.buildinfo 150c3140cc02c8de2463f5ac2d1b35d1 737648 science optional mafft_7.429-1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: mafft Binary: mafft Architecture: armhf Version: 7.429-1 Checksums-Md5: e1ca996338ec0860f32d63e6002c2add 9017964 mafft-dbgsym_7.429-1_armhf.deb 150c3140cc02c8de2463f5ac2d1b35d1 737648 mafft_7.429-1_armhf.deb Checksums-Sha1: 3a01bbe1532e02be6546db85677fb69f6617d5d9 9017964 mafft-dbgsym_7.429-1_armhf.deb 6e60ff8e1d6f25d5b6af5c4dde9d2d18b1965187 737648 mafft_7.429-1_armhf.deb Checksums-Sha256: 5344a5289985ba00e77a81a6a9098d68bfe1de93defadc9332e9cde26f7d908e 9017964 mafft-dbgsym_7.429-1_armhf.deb 8628022fb947fc284700eb845dfbc9fec10777196fb2d94d19533ef6d4706fae 737648 mafft_7.429-1_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 18 Sep 2019 01:04:57 +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 (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.32.51.20190909-1), binutils-common (= 2.32.51.20190909-1), binutils-x86-64-linux-gnu (= 2.32.51.20190909-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-22), cpp-9 (= 9.2.1-8), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.6.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-8), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-22), gcc-8-base (= 8.3.0-22), gcc-9 (= 9.2.1-8), gcc-9-base (= 9.2.1-8), 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+b1), hostname (= 3.22+b1), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.65-1), libasan5 (= 9.2.1-8), libatomic1 (= 9.2.1-8), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.32.51.20190909-1), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-1), libc-dev-bin (= 2.29-1), libc6 (= 2.29-1), libc6-dev (= 2.29-1), libcap-ng0 (= 0.7.9-2+b1), libcc1-0 (= 9.2.1-8), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdebhelper-perl (= 12.6.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.0-1), libgcc-8-dev (= 8.3.0-22), libgcc-9-dev (= 9.2.1-8), libgcc1 (= 1:9.2.1-8), libgcrypt20 (= 1.8.5-2), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.60.6-2), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-8), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-8), liblsan0 (= 9.2.1-8), liblz4-1 (= 1.8.3-1+b1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-22), libncurses6 (= 6.1+20190803-1), libncursesw6 (= 6.1+20190803-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.2.1-8), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-9-dev (= 9.2.1-8), libstdc++6 (= 9.2.1-8), libsub-override-perl (= 0.09-2), libsystemd0 (= 242-7), libtinfo6 (= 6.1+20190803-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-8), libubsan1 (= 9.2.1-8), libuchardet0 (= 0.0.6-3), libudev1 (= 242-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.2.9-2), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.7-3), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190803-1), ncurses-bin (= 6.1+20190803-1), patch (= 2.7.6-6), 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 (= 2.96~beta-1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1564224987" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ mafft-dbgsym_7.429-1_armhf.deb ------------------------------ new Debian package, version 2.0. size 9017964 bytes: control archive=2016 bytes. 1594 bytes, 12 lines control 3371 bytes, 32 lines md5sums Package: mafft-dbgsym Source: mafft Version: 7.429-1 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 11312 Depends: mafft (= 7.429-1) Section: debug Priority: optional Description: debug symbols for mafft Build-Ids: 04303aa0cb2f09b6a97b2943190136e4e8e67bdb 107bbd097b3e594ae72d4084e11747cbeeb400e7 10fceba6f1be1f24d9345a332535f914cc0b1107 16935fa978e1e548c249e7350476c58df44fcb1e 22dd415d82c430669e3fe85911dd5a672742089e 273ccf797ae7bf966a4ffafc268bbfb567bd9aca 34253e9f57dc88d0a9a40fa77877bdc9c08cf59b 498653c27e520f4c99b7210aaf26a36db717e63d 4a815de77486168ec394917397dc112f321dbd13 4c84cc73586c3d576eddb7b7ddab2c6dc0f7e180 66e727a2dd6121db33edd964cef616d542eda5e0 6ca922504817191afee041f998a6d4dc2253f370 6e798b0767a12e77b03e723318f6c7e7549eb448 72862e31bf1a4719fb62c5ca390cf475224c3414 85801296f2febe00e53978905991db9ae3abebc9 88d694429b8e028582704ce995f88fca7e141c49 8fd33ad91a6a5bf62ceadfd11bd4458af1d5c864 93f499a06cf5dca6b383109249a348d55afe0cd1 94ddd18967e72f7314429a8958efe6d4998c6711 9510469e2640a1c9484d67972c596f873b22f129 9f87325b2a1cef23deb8690f64b0c1b34d206532 a372daa069caec637864b9af0e8eec50faf0b8af 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./usr/lib/debug/.build-id/cf/3cb865879be966b05c0839a58e17197a7cf6c9.debug drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/debug/.build-id/e0/ -rw-r--r-- root/root 606148 2019-07-27 10:56 ./usr/lib/debug/.build-id/e0/4cc8f3eb5c524ebd98823a7797ab135779e79f.debug drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/debug/.build-id/e8/ -rw-r--r-- root/root 118932 2019-07-27 10:56 ./usr/lib/debug/.build-id/e8/b02b98dc721a5d43fba8d953be1e7a60789a7b.debug drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 318556 2019-07-27 10:56 ./usr/lib/debug/.build-id/f8/3d950d746ae60189b7a74131506c38c3afa772.debug drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 26372 2019-07-27 10:56 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/mafft.debug drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/doc/mafft-dbgsym -> mafft mafft_7.429-1_armhf.deb ----------------------- new Debian package, version 2.0. size 737648 bytes: control archive=2344 bytes. 1385 bytes, 30 lines control 3783 bytes, 54 lines md5sums Package: mafft Version: 7.429-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 7305 Depends: libc6 (>= 2.29), 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 2019-07-27 10:56 ./ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/bin/ lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/bin/mafft -> ../lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/bin/mafft-profile -> ../lib/mafft/bin/mafft-profile drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/mafft/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/ lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/einsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/fftns -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/fftnsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/ginsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/linsi -> mafft -rwxr-xr-x root/root 104699 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-einsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-fftns -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-ginsi -> mafft -rwxr-xr-x root/root 11551 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-linsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-nwns -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-qinsi -> mafft -rwxr-xr-x root/root 7788 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-sparsecore.rb lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/mafft-xinsi -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/nwns -> mafft lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/lib/mafft/bin/nwnsi -> mafft drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/mafft/lib/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/ -rwxr-xr-x root/root 357940 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/addsingle -rwxr-xr-x root/root 202292 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/contrafoldwrap -rwxr-xr-x root/root 59100 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/countlen -rwxr-xr-x root/root 366132 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/disttbfast -rwxr-xr-x root/root 210484 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/dndblast -rwxr-xr-x root/root 210484 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/dndfast7 -rwxr-xr-x root/root 202300 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/dndpre -rwxr-xr-x root/root 366132 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/dvtditr -rwxr-xr-x root/root 108084 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/f2cl -rwxr-xr-x root/root 325172 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/getlag -rwxr-xr-x root/root 5672 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/hex2maffttext -rwxr-xr-x root/root 210484 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/mafft-distance -rwxr-xr-x root/root 325172 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/mafft-profile -rwxr-xr-x root/root 10475 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/mafftash_premafft.pl -rwxr-xr-x root/root 5672 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/maffttext2hex -rwxr-xr-x root/root 337476 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/makedirectionlist -rwxr-xr-x root/root 206388 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/mccaskillwrap -rwxr-xr-x root/root 218676 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/multi2hat3s -rwxr-xr-x root/root 366132 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/nodepair -rwxr-xr-x root/root 337460 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/pairash -rwxr-xr-x root/root 353844 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/pairlocalalign -rwxr-xr-x root/root 157404 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/regtable2seq -rwxr-xr-x root/root 153308 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/replaceu -rwxr-xr-x root/root 157404 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/restoreu -rwxr-xr-x root/root 202292 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/score -rwxr-xr-x root/root 15541 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/seekquencer_premafft.pl -rwxr-xr-x root/root 59100 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/seq2regtable -rwxr-xr-x root/root 325172 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/setcore -rwxr-xr-x root/root 157412 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/setdirection -rwxr-xr-x root/root 210484 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/sextet5 -rwxr-xr-x root/root 345652 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/splittbfast -rwxr-xr-x root/root 394804 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/tbfast -rwxr-xr-x root/root 5672 2019-07-27 10:56 ./usr/lib/mafft/lib/mafft/version drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/doc/mafft/ -rw-r--r-- root/root 3634 2019-07-27 10:56 ./usr/share/doc/mafft/changelog.Debian.gz -rw-r--r-- root/root 1931 2019-07-27 10:56 ./usr/share/doc/mafft/copyright drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/doc/mafft/test/ -rw-r--r-- root/root 16616 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample -rw-r--r-- root/root 30112 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.dpparttree -rw-r--r-- root/root 28816 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.fftns2 -rw-r--r-- root/root 28996 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.fftnsi -rw-r--r-- root/root 29896 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.gins1 -rw-r--r-- root/root 29572 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.ginsi -rw-r--r-- root/root 41380 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.ginsi.allowshift -rw-r--r-- root/root 28888 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.lins1 -rw-r--r-- root/root 29500 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.linsi -rw-r--r-- root/root 30112 2019-07-01 06:59 ./usr/share/doc/mafft/test/sample.parttree -rw-r--r-- root/root 1502 2019-07-01 06:59 ./usr/share/doc/mafft/test/samplerna -rw-r--r-- root/root 1916 2019-07-01 06:59 ./usr/share/doc/mafft/test/samplerna.qinsi -rw-r--r-- root/root 1916 2019-07-01 06:59 ./usr/share/doc/mafft/test/samplerna.xinsi -rw-r--r-- root/root 725 2019-07-01 06:59 ./usr/share/doc/mafft/test/script drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/man/ drwxr-xr-x root/root 0 2019-07-27 10:56 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz -rw-r--r-- root/root 2130 2019-07-27 10:56 ./usr/share/man/man1/mafft-homologs.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2019-07-27 10:56 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz -rw-r--r-- root/root 4421 2019-07-27 10:56 ./usr/share/man/man1/mafft.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [533 B] Get:5 copy:/<>/apt_archive ./ Packages [617 B] Fetched 2113 B in 0s (98.9 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 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-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 libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-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 libclass-xsaccessor-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 8522 kB of archives. After this operation, 23.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.29.0-2 [646 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-1 [1533 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-1 [320 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.41-1 [79.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b1 [17.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.000008-1 [19.7 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006003-1 [19.7 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.80+repack-2 [34.5 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.21.0 [1258 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8522 kB in 0s (27.7 MB/s) Selecting previously unselected package readline-common. (Reading database ... 18961 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 111112 Build-Time: 74 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 17 Job: mafft_7.429-1 Lintian: pass Machine Architecture: amd64 Package: mafft Package-Time: 103 Source-Version: 7.429-1 Space: 111112 Status: successful Version: 7.429-1 -------------------------------------------------------------------------------- Finished at 2019-09-18T01:04:57Z Build needed 00:01:43, 111112k disk space