sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | kma 1.2.12-1 (armhf) Wed, 25 Sep 2019 00:13:21 +0000 | +==============================================================================+ Package: kma Version: 1.2.12-1 Source Version: 1.2.12-1 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-50ec5622-c5a0-4c6e-a72f-2220ae4ea369' with '<>' I: NOTICE: Log filtering will replace 'build/kma-ErFPkz/resolver-4QBfMq' 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 2019-09-24-0813.11.pdiff [5362 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-24-1416.36.pdiff [10.1 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-24-2013.54.pdiff [7165 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-09-24-2013.54.pdiff [7165 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-24-0813.11.pdiff [4835 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-24-1416.36.pdiff [8123 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-24-2013.54.pdiff [10.5 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-09-24-2013.54.pdiff [10.5 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armhf Packages [7994 kB] Fetched 8235 kB in 2s (4276 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libacl1 libattr1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 52.2 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libacl1 amd64 2.2.53-5 [30.7 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libattr1 amd64 1:2.4.48-5 [21.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.2 kB in 0s (0 B/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13083 files and directories currently installed.) Preparing to unpack .../libacl1_2.2.53-5_amd64.deb ... Unpacking libacl1:amd64 (2.2.53-5) over (2.2.53-4) ... Setting up libacl1:amd64 (2.2.53-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13083 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.4.48-5_amd64.deb ... Unpacking libattr1:amd64 (1:2.4.48-5) over (1:2.4.48-4) ... Setting up libattr1:amd64 (1:2.4.48-5) ... Processing triggers for libc-bin (2.29-2) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'kma' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/kam.git Please use: git clone https://salsa.debian.org/med-team/kam.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 731 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main kma 1.2.12-1 (dsc) [1918 B] Get:2 http://debian.oregonstate.edu/debian unstable/main kma 1.2.12-1 (tar) [724 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main kma 1.2.12-1 (diff) [4964 B] Fetched 731 kB in 0s (32.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/kma-ErFPkz/kma-1.2.12' with '<>' I: NOTICE: Log filtering will replace 'build/kma-ErFPkz' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, 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), zlib1g-dev, 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 [409 B] Get:5 copy:/<>/apt_archive ./ Packages [497 B] Fetched 1863 B in 0s (89.6 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 zlib1g:armhf zlib1g-dev:armhf 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 zlib1g:armhf zlib1g-dev:armhf 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 62.2 MB of archives. After this operation, 239 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 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 1.66-2 [103 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 2.29-2 [2341 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 2.29-2 [2141 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] Get:86 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1+b1 [85.1 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1+b1 [204 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.2 MB in 1s (70.0 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 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 (2.29-2) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up libc6-dev:armhf (2.29-2) ... Setting up libstdc++6:armhf (9.2.1-8) ... Setting up debhelper (12.6.1) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1+b1) ... 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 zlib1g-dev:armhf (1:1.2.11.dfsg-1+b1) ... 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 (2.29-2) ... +------------------------------------------------------------------------------+ | 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_2.29-2 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_1.8.4 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_1.45.4-1 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 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Team Uploaders: Andreas Tille Homepage: https://bitbucket.org/genomicepidemiology/kma Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/kma Vcs-Git: https://salsa.debian.org/med-team/kam.git Build-Depends: debhelper-compat (= 12), zlib1g-dev Package-List: kma deb science optional arch=any Checksums-Sha1: 805261fd57477641436163c8ecb9707dc0496698 724491 kma_1.2.12.orig.tar.bz2 52eb0dfd0156c1da306e38b2e2cfecc99dead94b 4964 kma_1.2.12-1.debian.tar.xz Checksums-Sha256: 8df51d1416922f91c5351a60a9d5e8c414a911a32af416ba70f1e4735648bd6c 724491 kma_1.2.12.orig.tar.bz2 2acaa3e35992673c77250381fb006dc4f3cd6b82cd110ff697e1bbff61c8259a 4964 kma_1.2.12-1.debian.tar.xz Files: 02570b24e963bfb83b17302523103976 724491 kma_1.2.12.orig.tar.bz2 b9e12eb1db0e1e3b4cad380900216c27 4964 kma_1.2.12-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl2If8ITHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0Wt/EACAbt7t9a3UGmloqSLIHhXhYUkfrVvD 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signature: No public key dpkg-source: warning: failed to verify signature on ./kma_1.2.12-1.dsc dpkg-source: info: extracting kma in /<> dpkg-source: info: unpacking kma_1.2.12.orig.tar.bz2 dpkg-source: info: unpacking kma_1.2.12-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.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-50ec5622-c5a0-4c6e-a72f-2220ae4ea369 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 kma dpkg-buildpackage: info: source version 1.2.12-1 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 dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -f align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmerlink.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o kma kma_index kma_shm kma_update libkma.a make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc make[1]: Entering directory '/<>' arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align.o align.c In file included from align.c:28: align.c: In function ‘KMA’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:90:55: note: in expansion of macro ‘getNuc’ 90 | for(j = i - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:103:51: note: in expansion of macro ‘getNuc’ 103 | while(i < end && value < t_len && qseq[i] == getNuc(template_index->seq, value)) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:143:56: note: in expansion of macro ‘getNuc’ 143 | for(j = k - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:156:52: note: in expansion of macro ‘getNuc’ 156 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) { | ^~~~~~ align.c: In function ‘KMA_score’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:453:54: note: in expansion of macro ‘getNuc’ 453 | for(k = j - 1; 0 <= k && 0 <= prev && qseq[k] == getNuc(template_index->seq, prev); --k) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:468:50: note: in expansion of macro ‘getNuc’ 468 | while(j < end && value < t_len && qseq[j] == getNuc(template_index->seq, value)) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:499:55: note: in expansion of macro ‘getNuc’ 499 | for(k = l - 1; 0 <= k && 0 <= prev && qseq[k] == getNuc(template_index->seq, prev); --k) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:513:51: note: in expansion of macro ‘getNuc’ 513 | while(l < end && value < t_len && qseq[l] == getNuc(template_index->seq, value)) { | ^~~~~~ align.c: In function ‘anker_rc’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:781:55: note: in expansion of macro ‘getNuc’ 781 | for(j = i - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:796:51: note: in expansion of macro ‘getNuc’ 796 | while(i < end && value < t_len && qseq[i] == getNuc(template_index->seq, value)) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:839:56: note: in expansion of macro ‘getNuc’ 839 | for(j = k - 1; 0 <= j && 0 <= prev && qseq[j] == getNuc(template_index->seq, prev); --j) { | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ align.c:852:52: note: in expansion of macro ‘getNuc’ 852 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) { | ^~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnfrags.o alnfrags.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ankers.o ankers.c ankers.c: In function ‘get_ankers’: ankers.c:202:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 202 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ankers.c:203:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 203 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ankers.c:204:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 204 | fread(out_Tem + 1, sizeof(int), *out_Tem, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ankers.c:205:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 205 | fread(header->seq, 1, header->len, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o assembly.o assembly.c In file included from assembly.c:36: assembly.c: In function ‘updateMatrix’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ assembly.c:122:72: note: in expansion of macro ‘getNuc’ 122 | check = sprintf(update, "%c\t%hu\t%hu\t%hu\t%hu\t%hu\t%hu\n", bases[getNuc(template_seq, i)], assembly[pos].counts[0], assembly[pos].counts[1], assembly[pos].counts[2], assembly[pos].counts[3], assembly[pos].counts[4], assembly[pos].counts[5]); | ^~~~~~ assembly.c: In function ‘assemble_KMA_threaded’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ assembly.c:646:32: note: in expansion of macro ‘getNuc’ 646 | aligned_assem->t[i] = bases[getNuc(template_index->seq, pos)]; | ^~~~~~ assembly.c: In function ‘assemble_KMA_dense_threaded’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ assembly.c:821:26: note: in expansion of macro ‘getNuc’ 821 | aligned_assem->t[i] = getNuc(template_index->seq, i); | ^~~~~~ assembly.c: In function ‘assemble_KMA_threaded’: assembly.c:388:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 388 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:415:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 415 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:416:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 416 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c: In function ‘assemble_KMA_dense_threaded’: assembly.c:862:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 862 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:889:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 889 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:890:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 890 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c: In function ‘skip_assemble_KMA’: assembly.c:1137:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1137 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1157:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1157 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1158:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1158 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o chain.o chain.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compdna.o compdna.c In file included from compdna.c:25: compdna.c: In function ‘unCompDNA’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ compdna.c:154:12: note: in expansion of macro ‘getNuc’ 154 | *--seq = getNuc(compressor->seq, i); | ^~~~~~ compdna.c: In function ‘binRev’: compdna.c:192:15: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | return ((mer >> 32) | (mer << 32)); | ^~ compdna.c:192:29: warning: left shift count >= width of type [-Wshift-count-overflow] 192 | return ((mer >> 32) | (mer << 32)); | ^~ compdna.c: In function ‘getComp’: compdna.c:289:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 289 | fread(&compressor->seqlen, sizeof(int), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compkmers.o compkmers.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compress.o compress.c compress.c: In function ‘compressKMA_DB’: compress.c:103:8: warning: right shift count >= width of type [-Wshift-count-overflow] 103 | check >>= 32; | ^~~ compress.c: In function ‘compressKMA_deconDB’: compress.c:939:9: warning: right shift count >= width of type [-Wshift-count-overflow] 939 | check >>= 32; | ^~~ compress.c: In function ‘compressKMA_deconMegaDB’: compress.c:1042:9: warning: right shift count >= width of type [-Wshift-count-overflow] 1042 | check >>= 32; | ^~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ef.o ef.c In file included from ef.c:25: ef.c: In function ‘getExtendedFeatures’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ ef.c:82:51: note: in expansion of macro ‘getNuc’ 82 | snpSum += (depthUpdate - assembly[pos].counts[getNuc(template_seq, pos)]); | ^~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filebuff.o filebuff.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o frags.o frags.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmap.o hashmap.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapindex.o hashmapindex.c hashmapindex.c: In function ‘hashMap_index_load’: hashmapindex.c:267:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 267 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hashmapindex.c:268:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 268 | read(index, src->index, src->size * sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hashmapindex.c: In function ‘hashMap_index_build’: hashmapindex.c:293:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 293 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hashmapindex.c: In function ‘alignLoad_shm_initial’: hashmapindex.c:369:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 369 | read(index_in, &kmersize, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkmers.o hashmapkmers.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c index.c: In function ‘index_main’: index.c:343:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 343 | fread(inputfiles[filecount - 1], 1, size - 1, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ index.c:396:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 396 | fread(deconfiles[deconcount - 1], 1, size - 1, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c kma.c: In function ‘kma_main’: kma.c:1093:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1093 | fread(&qseq.len, sizeof(int), 1, templatefile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ kma.c:1088:34: warning: argument 1 null where non-null expected [-Wnonnull] 1088 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabihf/include/string.h:384:15: note: in a call to function ‘strlen’ declared here 384 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1132:32: warning: argument 1 null where non-null expected [-Wnonnull] 1132 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabihf/include/string.h:384:15: note: in a call to function ‘strlen’ declared here 384 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1138:32: warning: argument 1 null where non-null expected [-Wnonnull] 1138 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabihf/include/string.h:384:15: note: in a call to function ‘strlen’ declared here 384 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1150:32: warning: argument 1 null where non-null expected [-Wnonnull] 1150 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabihf/include/string.h:384:15: note: in a call to function ‘strlen’ declared here 384 | extern size_t strlen (const char *__s) | ^~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmapipe.o kmapipe.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmerlink.o kmerlink.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmers.o kmers.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmmap.o kmmap.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loadupdate.o loadupdate.c loadupdate.c: In function ‘load_DBs’: loadupdate.c:178:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 178 | fread(&DB_size, sizeof(unsigned), 1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:183:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 183 | fread(*template_lengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:184:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 184 | fread(*template_slengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:185:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 185 | fread(*template_ulengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:193:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 193 | fread(*template_lengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c mt1.c: In function ‘runKMA_Mt1’: mt1.c:166:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 166 | fread(&DB_size, sizeof(int), 1, DB_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o nw.o nw.c In file included from nw.c:24: nw.c: In function ‘NW’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:73:21: note: in expansion of macro ‘getNuc’ 73 | aligned->t[m] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:161:11: note: in expansion of macro ‘getNuc’ 161 | t_nuc = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:258:27: note: in expansion of macro ‘getNuc’ 258 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:266:28: note: in expansion of macro ‘getNuc’ 266 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:273:27: note: in expansion of macro ‘getNuc’ 273 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ nw.c: In function ‘NW_band’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:349:21: note: in expansion of macro ‘getNuc’ 349 | aligned->t[m] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:452:11: note: in expansion of macro ‘getNuc’ 452 | t_nuc = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:585:27: note: in expansion of macro ‘getNuc’ 585 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:593:28: note: in expansion of macro ‘getNuc’ 593 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:601:27: note: in expansion of macro ‘getNuc’ 601 | aligned->t[Stat.len] = getNuc(template, nuc_pos); | ^~~~~~ nw.c: In function ‘NW_score’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:748:11: note: in expansion of macro ‘getNuc’ 748 | t_nuc = getNuc(template, nuc_pos); | ^~~~~~ nw.c: In function ‘NW_band_score’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ nw.c:1003:11: note: in expansion of macro ‘getNuc’ 1003 | t_nuc = getNuc(template, nuc_pos); | ^~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pherror.o pherror.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qseqs.o qseqs.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qualcheck.o qualcheck.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runinput.o runinput.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c runkma.c: In function ‘runKMA’: runkma.c:216:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 216 | read(index_in_no, &kmersize, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:573:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 573 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:574:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 574 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:575:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 575 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:576:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 576 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:577:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 577 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:672:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 672 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:676:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 676 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:677:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 677 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:721:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 721 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:774:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 774 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:817:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 817 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:841:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 841 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:857:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 857 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:858:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 858 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:859:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 859 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:860:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 860 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:861:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 861 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1007:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1007 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1011:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1011 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1012:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1012 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c: In function ‘runKMA_MEM’: runkma.c:1346:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1346 | read(index_in_no, &kmersize, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1591:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1591 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1592:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1592 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1593:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1593 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1594:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1594 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1595:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1595 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1690:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1690 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1694:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1694 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1695:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1695 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1739:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1739 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1792:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1792 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1835:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1835 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1859:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1859 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1875:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1875 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1876:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1876 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1877:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1877 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1878:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1878 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1879:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1879 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2025:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2025 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2029:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2029 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2030:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2030 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c savekmers.c: In function ‘loadFsa’: savekmers.c:84:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 84 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ savekmers.c:85:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 85 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ savekmers.c:86:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 86 | fread(header->seq, 1, header->len, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seq2fasta.o seq2fasta.c In file included from seq2fasta.c:28: seq2fasta.c: In function ‘printFastas’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ seq2fasta.c:89:19: note: in expansion of macro ‘getNuc’ 89 | *--seq = bases[getNuc(compseq, j)]; | ^~~~~~ seq2fasta.c: In function ‘printFastaList’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ seq2fasta.c:151:20: note: in expansion of macro ‘getNuc’ 151 | *--seq = bases[getNuc(compseq, j)]; | ^~~~~~ seq2fasta.c: In function ‘printFastas’: seq2fasta.c:84:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 84 | fread(compseq, sizeof(long unsigned), (template_lengths[i] >> 5) + 1, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seq2fasta.c: In function ‘printFastaList’: seq2fasta.c:146:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 146 | fread(compseq, sizeof(long unsigned), (template_lengths[i] >> 5) + 1, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqmenttree.o seqmenttree.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqparse.o seqparse.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o shm.o shm.c shm.c: In function ‘hashMapKMA_setupSHM’: shm.c:95:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 95 | fread(dest->exist, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c:115:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 115 | fread(dest->values, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c:138:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 138 | fread(dest->key_index, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c:158:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 158 | fread(dest->value_index, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c: In function ‘length_setupSHM’: shm.c:263:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 263 | fread(template_lengths, sizeof(unsigned), size / sizeof(unsigned), file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c: In function ‘index_setupSHM’: shm.c:305:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 305 | fread(index, sizeof(int), size / sizeof(int), file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c: In function ‘seq_setupSHM’: shm.c:346:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 346 | fread(seq, sizeof(long unsigned), size / sizeof(long unsigned), file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c: In function ‘name_setupSHM’: shm.c:388:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 388 | fread(template_names, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sparse.o sparse.c sparse.c: In function ‘load_DBs_Sparse’: sparse.c:156:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 156 | fread(*template_lengths, sizeof(int), DB_size, DB_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sparse.c:157:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 157 | fread(*template_ulengths, sizeof(int), DB_size, DB_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sparse.c:197:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 197 | fread(template_names[0], 1, file_size, DB_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c spltdb.c: In function ‘runKMA_spltDB’: spltdb.c:460:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 460 | fread(template_lengths + dbBiases[i], sizeof(int), bias, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:849:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 849 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:850:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 850 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:851:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 851 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:852:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 852 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:853:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 853 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:948:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 948 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:952:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 952 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:953:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 953 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:997:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 997 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1050:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1050 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1093:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1093 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1117:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1117 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1133:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1133 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1134:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1134 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1135:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1135 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1136:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1136 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1137:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1137 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1281:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1281 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1285:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1285 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1286:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1286 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1525:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1525 | read(index_in_no, &kmersize, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1569:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 1569 | read(index_in_no, &kmersize, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdnuc.o stdnuc.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdstat.o stdstat.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp.o tmp.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update.o update.c update.c: In function ‘convertLength_014to015’: update.c:40:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 40 | fread(&size, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c: In function ‘hashMapKMA_014to015’: update.c:88:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 88 | fread(&DB_size, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:89:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 89 | fread(&dest->kmersize, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:90:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 90 | fread(&dest->prefix_len, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:91:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 91 | fread(&dest->prefix, sizeof(long unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:92:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 92 | fread(&dest->size, sizeof(long unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:100:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 100 | fread(&tmp, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:102:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 102 | fread(&seqsize, sizeof(unsigned), 1, file); //seq size | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:103:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 103 | fread(&tmp, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ update.c:105:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 105 | fread(&tmp, sizeof(unsigned), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updateindex.o updateindex.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updatescores.o updatescores.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o valueshash.o valueshash.c arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c In file included from vcf.c:26: vcf.c: In function ‘updateVcf’: stdnuc.h:20:65: warning: right shift count >= width of type [-Wshift-count-overflow] 20 | #define getNuc(Comp,pos) ((Comp[pos >> 5] << ((pos & 31) << 1)) >> 62) | ^~ vcf.c:122:16: note: in expansion of macro ‘getNuc’ 122 | nuc = bases[getNuc(template_seq, pos)]; | ^~~~~~ ar -csru libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmerlink.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o ar: `u' modifier ignored since `D' is the default (see `U') arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -o kma main.c libkma.a -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -o kma_index kma_index.c libkma.a -lm -lz -Wl,-z,relro -Wl,-z,now arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -o kma_shm kma_shm.c libkma.a -Wl,-z,relro -Wl,-z,now arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c99 -o kma_update kma_update.c libkma.a -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 252107 new size 253592 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kma' in '../kma_1.2.12-1_armhf.deb'. dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.2.12-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../kma_1.2.12-1_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 2019-09-25T00:14:18Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kma_1.2.12-1_armhf.changes: --------------------------- Format: 1.8 Date: Mon, 23 Sep 2019 09:58:31 +0200 Source: kma Binary: kma kma-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 1.2.12-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: kma - mapping genomic sequences to raw reads directly against redundant Changes: kma (1.2.12-1) unstable; urgency=medium . * Team upload. * New upstream version Checksums-Sha1: acc2175d6bd2631da4eb31fc0ff5832a1804b255 366792 kma-dbgsym_1.2.12-1_armhf.deb e20080d963ffbf0826efb9db3c2ce9d36350e5a0 4666 kma_1.2.12-1_armhf.buildinfo c9f797647d44ff7e5c6cab4b3503795f0e711a26 110472 kma_1.2.12-1_armhf.deb Checksums-Sha256: d185d040d4a7b43b69128a56871c11ae5d84dbb54f0c6062c8c4131b55f9fff4 366792 kma-dbgsym_1.2.12-1_armhf.deb 061082ef74ff71e6dd06e87b6a7d6fc7de8d251ebcefac367bfc2e6cd7d472f2 4666 kma_1.2.12-1_armhf.buildinfo 46347ebd6275206bdd1c2727716c21237d5b6bdb9aadd74382924c1794983aa9 110472 kma_1.2.12-1_armhf.deb Files: 1891ca0abb19ddf76c2fc047dc7dbed7 366792 debug optional kma-dbgsym_1.2.12-1_armhf.deb 2008b9a75e7f71fd927d387865ed3909 4666 science optional kma_1.2.12-1_armhf.buildinfo b1b5f50394bc2851c8954f70b07c0cb0 110472 science optional kma_1.2.12-1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kma Binary: kma Architecture: armhf Version: 1.2.12-1 Checksums-Md5: 1891ca0abb19ddf76c2fc047dc7dbed7 366792 kma-dbgsym_1.2.12-1_armhf.deb b1b5f50394bc2851c8954f70b07c0cb0 110472 kma_1.2.12-1_armhf.deb Checksums-Sha1: acc2175d6bd2631da4eb31fc0ff5832a1804b255 366792 kma-dbgsym_1.2.12-1_armhf.deb c9f797647d44ff7e5c6cab4b3503795f0e711a26 110472 kma_1.2.12-1_armhf.deb Checksums-Sha256: d185d040d4a7b43b69128a56871c11ae5d84dbb54f0c6062c8c4131b55f9fff4 366792 kma-dbgsym_1.2.12-1_armhf.deb 46347ebd6275206bdd1c2727716c21237d5b6bdb9aadd74382924c1794983aa9 110472 kma_1.2.12-1_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 25 Sep 2019 00:14:17 +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 (= 2.2.53-5), libarchive-zip-perl (= 1.66-2), libasan5 (= 9.2.1-8), libatomic1 (= 9.2.1-8), libattr1 (= 1:2.4.48-5), 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 (= 2.29-2), libc-dev-bin (= 2.29-2), libc6 (= 2.29-2), libc6-dev (= 2.29-2), 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), zlib1g-dev (= 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="1569225511" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kma-dbgsym_1.2.12-1_armhf.deb ----------------------------- new Debian package, version 2.0. size 366792 bytes: control archive=692 bytes. 438 bytes, 12 lines control 401 bytes, 4 lines md5sums Package: kma-dbgsym Source: kma Version: 1.2.12-1 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 402 Depends: kma (= 1.2.12-1) Section: debug Priority: optional Description: debug symbols for kma Build-Ids: 11cbb72e88d7cabfbb5dc309c1649727b39385bb 477eee8a0f162d0f662aa9b33cccfb2adbdecb4a e6ab6dff1d25ffd47fba131dca703b330c403f72 drwxr-xr-x root/root 0 2019-09-23 07:58 ./ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/11/ -rw-r--r-- root/root 22436 2019-09-23 07:58 ./usr/lib/debug/.build-id/11/cbb72e88d7cabfbb5dc309c1649727b39385bb.debug drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/47/ -rw-r--r-- root/root 360696 2019-09-23 07:58 ./usr/lib/debug/.build-id/47/7eee8a0f162d0f662aa9b33cccfb2adbdecb4a.debug drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.build-id/e6/ -rw-r--r-- root/root 9016 2019-09-23 07:58 ./usr/lib/debug/.build-id/e6/ab6dff1d25ffd47fba131dca703b330c403f72.debug drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 3896 2019-09-23 07:58 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/kma.debug drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-09-23 07:58 ./usr/share/doc/kma-dbgsym -> kma kma_1.2.12-1_armhf.deb ---------------------- new Debian package, version 2.0. size 110472 bytes: control archive=1064 bytes. 883 bytes, 17 lines control 543 bytes, 9 lines md5sums Package: kma Version: 1.2.12-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 208 Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://bitbucket.org/genomicepidemiology/kma Description: mapping genomic sequences to raw reads directly against redundant databases KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particularly good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non- unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes. drwxr-xr-x root/root 0 2019-09-23 07:58 ./ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/bin/ -rwxr-xr-x root/root 173700 2019-09-23 07:58 ./usr/bin/kma -rwxr-xr-x root/root 5672 2019-09-23 07:58 ./usr/bin/kma_index -rwxr-xr-x root/root 13864 2019-09-23 07:58 ./usr/bin/kma_shm drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/doc/kma/ -rw-r--r-- root/root 2989 2019-09-09 07:18 ./usr/share/doc/kma/README.md.gz -rw-r--r-- root/root 323 2019-09-23 07:58 ./usr/share/doc/kma/changelog.Debian.gz -rw-r--r-- root/root 952 2019-09-23 07:58 ./usr/share/doc/kma/copyright drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/man/ drwxr-xr-x root/root 0 2019-09-23 07:58 ./usr/share/man/man1/ -rw-r--r-- root/root 1312 2019-09-23 07:58 ./usr/share/man/man1/kma.1.gz -rw-r--r-- root/root 697 2019-09-23 07:58 ./usr/share/man/man1/kma_index.1.gz -rw-r--r-- root/root 426 2019-09-23 07:58 ./usr/share/man/man1/kma_shm.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 [539 B] Get:5 copy:/<>/apt_archive ./ Packages [626 B] Fetched 2128 B in 0s (110 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 8525 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 [852 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 2.23.0 [1261 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8525 kB in 0s (27.6 MB/s) Selecting previously unselected package readline-common. (Reading database ... 18995 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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Setting up libio-pty-perl (1:1.08-1.1+b5) ... Setting up libclone-perl (0.41-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libssl1.1:amd64 (1.1.1d-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libsqlite3-0:amd64 (3.29.0-2) ... Setting up libfuture-perl (0.41-1) ... Setting up libyaml-libyaml-perl (0.80+repack-2) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.3-7) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libio-async-perl (0.74-1) ... Setting up patchutils (0.3.4-2+b1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.25-4) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up t1utils (1.41-3) ... Setting up liblinux-epoll-perl (0.016-1+b1) ... Setting up diffstat (1.62-1+b1) ... Setting up libb-hooks-op-check-perl (0.22-1+b1) ... Setting up libipc-run-perl (20180523.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsub-name-perl (0.21-1+b3) ... Setting up libpath-tiny-perl (0.108-1) ... Setting up librole-tiny-perl (2.000008-1) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up netbase (5.6) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006003-1) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-3) ... Setting up liburi-perl (1.76-1) ... Setting up libnet-ssleay-perl (1.88-1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b4) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libtype-tiny-perl (1.004004-1) ... Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up gpg (2.2.17-3) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003004-2) ... Setting up lintian (2.23.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.29-2) ... 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: 8020 Build-Time: 28 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 17 Job: kma_1.2.12-1 Lintian: pass Machine Architecture: amd64 Package: kma Package-Time: 57 Source-Version: 1.2.12-1 Space: 8020 Status: successful Version: 1.2.12-1 -------------------------------------------------------------------------------- Finished at 2019-09-25T00:14:18Z Build needed 00:00:57, 8020k disk space