sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | kma 1.3.0-1 (armel) Mon, 06 Jul 2020 10:08:06 +0000 | +==============================================================================+ Package: kma Version: 1.3.0-1 Source Version: 1.3.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-0fcc4d5c-6deb-4e41-851c-266b0ffd7378' with '<>' I: NOTICE: Log filtering will replace 'build/kma-8jpuq8/resolver-xTPcV3' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 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 2020-07-06-0801.46.pdiff [5066 B] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-07-06-0801.46.pdiff [5066 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-07-06-0801.46.pdiff [4316 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-07-06-0801.46.pdiff [4316 B] Get:6 http://debian.oregonstate.edu/debian unstable/main armel Packages [7929 kB] Fetched 8140 kB in 2s (5334 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: '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 743 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main kma 1.3.0-1 (dsc) [1911 B] Get:2 http://debian.oregonstate.edu/debian unstable/main kma 1.3.0-1 (tar) [736 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main kma 1.3.0-1 (diff) [4724 B] Fetched 743 kB in 0s (38.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/kma-8jpuq8/kma-1.3.0' with '<>' I: NOTICE: Log filtering will replace 'build/kma-8jpuq8' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [410 B] Get:5 copy:/<>/apt_archive ./ Packages [497 B] Fetched 1864 B in 0s (71.3 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-gnueabi bsdextrautils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu67 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db perl perl-modules-5.30 po-debconf sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-9-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel gnupg git bzr libstdc++-9-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:armel libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu67 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db perl perl-modules-5.30 po-debconf sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 88.5 MB of archives. After this operation, 366 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.35.2-6 [129 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10.1.0-4 [197 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.3.0-14 [197 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-3 [801 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-8 [2747 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-14 [1701 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-14 [10.7 MB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.3 [1468 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.3 [1905 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.3.0-13cross1 [197 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.3.0-13cross1 [6820 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3.1 [39.9 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-13cross1 [193 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.1.0-3cross1 [194 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.30-2cross1 [1128 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10.1.0-3cross1 [38.4 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10.1.0-3cross1 [84.5 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10.1.0-3cross1 [8804 B] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.3.0-13cross1 [341 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10.1.0-3cross1 [368 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10.1.0-3cross1 [114 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.3.0-13cross1 [644 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.3.0-13cross1 [7181 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.19-1cross1 [1155 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.30-2cross1 [2148 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.3.0-13cross1 [1714 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.3.0-13cross1 [7403 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-2 [8610 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5+b1 [710 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3.1 [38.9 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3.1 [49.9 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.2 [187 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.1-2 [38.2 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.1-2 [15.1 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.3-2 [1343 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.2 [1007 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10.1.0-4 [38.4 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.16-1 [101 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.30-8 [2348 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.3.0-14 [347 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10.1.0-4 [9016 B] Get:91 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.7.6-1 [1096 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.16-1 [120 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.30-8 [2189 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10.1.0-4 [86.2 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10.1.0-4 [409 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10.1.0-4 [115 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.3.0-14 [644 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.3.0-14 [1745 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.5 MB in 1s (112 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10481 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.35.2-6_amd64.deb ... Unpacking bsdextrautils (2.35.2-6) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../05-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../99-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-1) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up binutils-arm-linux-gnueabi (2.34-8) ... Setting up perl-modules-5.30 (5.30.3-4) ... Setting up bsdextrautils (2.35.2-6) ... Setting up libicu67:amd64 (67.1-2) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libglib2.0-0:amd64 (2.64.3-2) ... No schema files found: doing nothing. Setting up libmagic1:amd64 (1:5.38-5) ... Setting up linux-libc-dev:armel (5.7.6-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-5) ... Setting up linux-libc-dev-armel-cross (5.4.19-1cross1) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.3.0-13cross1) ... Setting up gcc-10-base:armel (10.1.0-4) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.3.0-13cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.3.0-13cross1) ... Setting up gcc-10-cross-base (10.1.0-3cross1) ... Setting up libc6-armel-cross (2.30-2cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.16-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up libc6-dev:amd64 (2.30-8) ... Setting up libc6-dev-armel-cross (2.30-2cross1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5+b1) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.3.0-14) ... Setting up libgomp1-armel-cross (10.1.0-3cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-14) ... Setting up libtool (2.4.6-14) ... Setting up libgcc-s1-armel-cross (10.1.0-3cross1) ... Setting up m4 (1.4.18-4) ... Setting up libstdc++6-armel-cross (10.1.0-3cross1) ... Setting up libatomic1-armel-cross (10.1.0-3cross1) ... Setting up perl (5.30.3-4) ... Setting up libasan5-armel-cross (9.3.0-13cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libubsan1-armel-cross (10.1.0-3cross1) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0043) ... Setting up g++-9 (9.3.0-14) ... Setting up libgcc-9-dev-armel-cross (9.3.0-13cross1) ... Setting up libdpkg-perl (1.20.3) ... Setting up autoconf (2.69-11.1) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up automake (1:1.16.2-3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.2) ... Setting up libstdc++-9-dev-armel-cross (9.3.0-13cross1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gcc-9-arm-linux-gnueabi (9.3.0-13cross1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up g++-9-arm-linux-gnueabi (9.3.0-13cross1) ... Setting up dpkg-dev (1.20.3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up build-essential (12.8) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-2) ... Setting up po-debconf (1.0.21) ... 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 g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... 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 dh-strip-nondeterminism (1.8.1-2) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3.1) ... Setting up dpkg-cross (2.6.15-3.1) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.16-1) ... Setting up libgcc-s1:armel (10.1.0-4) ... Setting up libc6:armel (2.30-8) ... Setting up libcrypt-dev:armel (1:4.4.16-1) ... Setting up libc6-dev:armel (2.30-8) ... Setting up libstdc++6:armel (10.1.0-4) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libgomp1:armel (10.1.0-4) ... Setting up dh-autoreconf (19) ... Setting up libasan5:armel (9.3.0-14) ... Setting up libatomic1:armel (10.1.0-4) ... Setting up libubsan1:armel (10.1.0-4) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up debhelper (13.2) ... Setting up libgcc-9-dev:armel (9.3.0-14) ... Setting up libstdc++-9-dev:armel (9.3.0-14) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2 (2020-04-29) amd64 (x86_64) Toolchain package versions: binutils_2.34-8 dpkg-dev_1.20.3 g++-9_9.3.0-14 gcc-9_9.3.0-14 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-14 libstdc++-9-dev-armel-cross_9.3.0-13cross1 libstdc++6_10.1.0-4 libstdc++6-armel-cross_10.1.0-3cross1 linux-libc-dev_5.7.6-1 Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8 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SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kma Binary: kma Architecture: any Version: 1.3.0-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://bitbucket.org/genomicepidemiology/kma Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kma Vcs-Git: https://salsa.debian.org/med-team/kam.git Build-Depends: debhelper-compat (= 13), zlib1g-dev Package-List: kma deb science optional arch=any Checksums-Sha1: a7c1c81c73559eb01e57c8d25b366cbf097cd11a 736115 kma_1.3.0.orig.tar.bz2 36b711273a272d11c88e8c4da190fe2b221882b3 4724 kma_1.3.0-1.debian.tar.xz Checksums-Sha256: 743ced8b18d60d866a10adbc3a244b6fc5974805fd6600594c1ce04d1107b31b 736115 kma_1.3.0.orig.tar.bz2 61b21f75eeb243bb68071e9b0f27c55802443de882073a30618cc2aab2ccf5ab 4724 kma_1.3.0-1.debian.tar.xz Files: e5a3c3acc6b2607c464a2c3eab93b965 736115 kma_1.3.0.orig.tar.bz2 5e955255e4c34aa76e3be9543e94aa3d 4724 kma_1.3.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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12:32:23 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kma_1.3.0-1.dsc dpkg-source: info: extracting kma in /<> dpkg-source: info: unpacking kma_1.3.0.orig.tar.bz2 dpkg-source: info: unpacking kma_1.3.0-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel 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-0fcc4d5c-6deb-4e41-851c-266b0ffd7378 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package kma dpkg-buildpackage: info: source version 1.3.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi 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 armel 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 dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.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 xml.o kma kma_index kma_shm kma_update libkma.a make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-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-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc make[1]: Entering directory '/<>' arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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:91:55: note: in expansion of macro ‘getNuc’ 91 | 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:104:51: note: in expansion of macro ‘getNuc’ 104 | 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:144:56: note: in expansion of macro ‘getNuc’ 144 | 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:157:52: note: in expansion of macro ‘getNuc’ 157 | 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:468:55: note: in expansion of macro ‘getNuc’ 468 | 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:483:51: note: in expansion of macro ‘getNuc’ 483 | 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:513:56: note: in expansion of macro ‘getNuc’ 513 | 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:527:52: note: in expansion of macro ‘getNuc’ 527 | 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:818:55: note: in expansion of macro ‘getNuc’ 818 | 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:833:51: note: in expansion of macro ‘getNuc’ 833 | 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:876:56: note: in expansion of macro ‘getNuc’ 876 | 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:889:52: note: in expansion of macro ‘getNuc’ 889 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) { | ^~~~~~ align.c: In function ‘anker_rc_comp’: 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:1008:55: note: in expansion of macro ‘getNuc’ 1008 | 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:1023:51: note: in expansion of macro ‘getNuc’ 1023 | 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:1059:56: note: in expansion of macro ‘getNuc’ 1059 | 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:1072:52: note: in expansion of macro ‘getNuc’ 1072 | while(k < end && value < t_len && qseq[k] == getNuc(template_index->seq, value)) { | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnfrags.o alnfrags.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o assembly.o assembly.c In file included from assembly.c:38: 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:121:72: note: in expansion of macro ‘getNuc’ 121 | 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:686:32: note: in expansion of macro ‘getNuc’ 686 | 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:858:26: note: in expansion of macro ‘getNuc’ 858 | aligned_assem->t[i] = getNuc(template_index->seq, i); | ^~~~~~ 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:1124:13: note: in expansion of macro ‘getNuc’ 1124 | bestNuc = getNuc(template_index->seq, i); | ^~~~~~ assembly.c: In function ‘callConsensus’: 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:1476:34: note: in expansion of macro ‘getNuc’ 1476 | aligned_assem->t[i] = bases[getNuc(seq, pos)]; | ^~~~~~ assembly.c: In function ‘assemble_KMA_threaded’: assembly.c:370:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 370 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:391:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 391 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:392:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 392 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c: In function ‘assemble_KMA_dense_threaded’: assembly.c:915:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 915 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:942:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 942 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:943:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 943 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c: In function ‘skip_assemble_KMA’: assembly.c:1238:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1238 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1258:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1258 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1259:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1259 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c: In function ‘assemble_KMA’: assembly.c:1794:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1794 | fread(buffer, sizeof(int), 8, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1815:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1815 | fread(qseq->seq, 1, qseq->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ assembly.c:1816:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1816 | fread(header->seq, 1, header->len, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o chain.o chain.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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:187:12: note: in expansion of macro ‘getNuc’ 187 | *--seq = getNuc(compressor->seq, i); | ^~~~~~ compdna.c: In function ‘binRev’: compdna.c:225:15: warning: right shift count >= width of type [-Wshift-count-overflow] 225 | return ((mer >> 32) | (mer << 32)); | ^~ compdna.c:225:29: warning: left shift count >= width of type [-Wshift-count-overflow] 225 | return ((mer >> 32) | (mer << 32)); | ^~ compdna.c: In function ‘getComp’: compdna.c:322:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 322 | fread(&compressor->seqlen, sizeof(int), 1, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compkmers.o compkmers.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compress.o compress.c compress.c: In function ‘compressKMA_DB’: compress.c:105:8: warning: right shift count >= width of type [-Wshift-count-overflow] 105 | check >>= 32; | ^~~ compress.c: In function ‘compressKMA_deconDB’: compress.c:941:9: warning: right shift count >= width of type [-Wshift-count-overflow] 941 | check >>= 32; | ^~~ compress.c: In function ‘compressKMA_deconMegaDB’: compress.c:1044:9: warning: right shift count >= width of type [-Wshift-count-overflow] 1044 | check >>= 32; | ^~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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:95:52: note: in expansion of macro ‘getNuc’ 95 | snpSum += (depthUpdate - assembly[pos].counts[getNuc(seq, pos)]); | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filebuff.o filebuff.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o frags.o frags.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmap.o hashmap.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapcci.o hashmapcci.c hashmapcci.c: In function ‘hashMapCCI_initialize’: hashmapcci.c:54:15: warning: right shift count >= width of type [-Wshift-count-overflow] 54 | size |= size >> 32; | ^~ hashmapcci.c: In function ‘hashMapCCI_load’: hashmapcci.c:472:2: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 472 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hashmapcci.c: In function ‘hashMapCCI_load_thread’: hashmapcci.c:499:3: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 499 | read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkmers.o hashmapkmers.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c index.c: In function ‘index_main’: index.c:340:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 340 | fread(inputfiles[filecount - 1], 1, size - 1, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ index.c:390:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 390 | fread(deconfiles[deconcount - 1], 1, size - 1, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c kma.c: In function ‘kma_main’: kma.c:1143:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1143 | fread(&qseq.len, sizeof(int), 1, templatefile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ kma.c:1138:34: 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-gnueabi/include/string.h:385:15: note: in a call to function ‘strlen’ declared here 385 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1184:32: warning: argument 1 null where non-null expected [-Wnonnull] 1184 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabi/include/string.h:385:15: note: in a call to function ‘strlen’ declared here 385 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1190:32: warning: argument 1 null where non-null expected [-Wnonnull] 1190 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabi/include/string.h:385:15: note: in a call to function ‘strlen’ declared here 385 | extern size_t strlen (const char *__s) | ^~~~~~ kma.c:1202:32: warning: argument 1 null where non-null expected [-Wnonnull] 1202 | myTemplatefilename = smalloc(strlen(templatefilename) + 64); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kma.c:22: /usr/arm-linux-gnueabi/include/string.h:385:15: note: in a call to function ‘strlen’ declared here 385 | extern size_t strlen (const char *__s) | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmapipe.o kmapipe.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmers.o kmers.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmmap.o kmmap.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loadupdate.o loadupdate.c loadupdate.c: In function ‘load_DBs’: loadupdate.c:175:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 175 | fread(&DB_size, sizeof(unsigned), 1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:180:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 180 | fread(*template_lengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:181:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 181 | fread(*template_slengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:182:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 182 | fread(*template_ulengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ loadupdate.c:190:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 190 | fread(*template_lengths, sizeof(unsigned), DB_size, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o matrix.o matrix.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c mt1.c: In function ‘runKMA_Mt1’: mt1.c:178:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 178 | fread(&DB_size, sizeof(int), 1, DB_file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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:450:11: note: in expansion of macro ‘getNuc’ 450 | 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:577:27: note: in expansion of macro ‘getNuc’ 577 | 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:585:28: 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:593:27: note: in expansion of macro ‘getNuc’ 593 | 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:740:11: note: in expansion of macro ‘getNuc’ 740 | 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:994:11: note: in expansion of macro ‘getNuc’ 994 | t_nuc = getNuc(template, nuc_pos); | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pherror.o pherror.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qseqs.o qseqs.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qualcheck.o qualcheck.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runinput.o runinput.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c runkma.c: In function ‘runKMA’: runkma.c:576:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 576 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:577:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 577 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:578:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 578 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:579:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 579 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:580:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 580 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:675:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 675 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:679:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 679 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:680:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 680 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:724:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 724 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:777:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 777 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:820:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 820 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:844:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 844 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:860:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 860 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:861:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 861 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:862:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 862 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:863:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 863 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:864:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 864 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1010:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1010 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1014:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1014 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1015:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1015 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c: In function ‘runKMA_MEM’: runkma.c:1657:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1657 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1658:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1658 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1659:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1659 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1660:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1660 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1661:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1661 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1756:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1756 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1760:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1760 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1761:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1761 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1805:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1805 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1858:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1858 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1901:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1901 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1925:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1925 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1941:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1941 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1942:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1942 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1943:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1943 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1944:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1944 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:1945:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1945 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2088:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2088 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2092:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2092 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runkma.c:2093:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 2093 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c savekmers.c: In function ‘loadFsa’: savekmers.c:83:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 83 | fread(qseq->seq, sizeof(long unsigned), qseq->complen, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ savekmers.c:84:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 84 | fread(qseq->N + 1, sizeof(int), qseq->N[0], inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ savekmers.c:85:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 85 | fread(header->seq, 1, header->len, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqmenttree.o seqmenttree.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqparse.o seqparse.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 ‘seq_setupSHM’: shm.c:305:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 305 | fread(seq, sizeof(long unsigned), size / sizeof(long unsigned), file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shm.c: In function ‘name_setupSHM’: shm.c:347:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 347 | fread(template_names, 1, size, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c spltdb.c: In function ‘runKMA_spltDB’: spltdb.c:461:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 461 | fread(template_lengths + dbBiases[i], sizeof(int), bias, inputfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:875:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 875 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:876:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 876 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:877:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 877 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:878:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 878 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:879:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 879 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:974:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 974 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:978:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 978 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:979:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 979 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1023:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1023 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1076:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1076 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1119:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1119 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1143:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1143 | fread(stats, sizeof(int), 2, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1159:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1159 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1160:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1160 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1161:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1161 | fread(best_start_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1162:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1162 | fread(best_end_pos, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1163:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1163 | fread(bestTemplates, sizeof(int), bestHits, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1307:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1307 | fread(stats, sizeof(int), 3, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1311:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1311 | fread(qseq->seq, 1, qseq->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spltdb.c:1312:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 1312 | fread(header->seq, 1, header->len, frag_in_raw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdnuc.o stdnuc.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdstat.o stdstat.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp.o tmp.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updateindex.o updateindex.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updatescores.o updatescores.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o valueshash.o valueshash.c arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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:123:16: note: in expansion of macro ‘getNuc’ 123 | nuc = bases[getNuc(template_seq, pos)]; | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xml.o xml.c ar -csru libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.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 xml.o ar: `u' modifier ignored since `D' is the default (see `U') arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma main.c libkma.a -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_index kma_index.c libkma.a -lm -lz -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_shm kma_shm.c libkma.a -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -o kma_update kma_update.c libkma.a -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp 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 -a dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 277624 new size 279208 dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'kma' in '../kma_1.3.0-1_armel.deb'. dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.3.0-1_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../kma_1.3.0-1_armel.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 2020-07-06T10:08:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ kma_1.3.0-1_armel.changes: -------------------------- Format: 1.8 Date: Sun, 05 Jul 2020 14:31:19 +0200 Source: kma Binary: kma kma-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 1.3.0-1 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 (1.3.0-1) unstable; urgency=medium . * Team upload. * New upstream version * debhelper-compat 13 (routine-update) Checksums-Sha1: 995136a2c89dabbfe82f4efa2d559e82635d9433 386400 kma-dbgsym_1.3.0-1_armel.deb 5624aed6d750d0504bc2acacfd2256ab64571129 4668 kma_1.3.0-1_armel.buildinfo 40c3c8dedf8e7705f3a0244585aa8ce139b9695b 121704 kma_1.3.0-1_armel.deb Checksums-Sha256: 7a80010d08449b6a8a37bb3dc5ed2bacdaadaa1951a00528814d4e390a1b0cbb 386400 kma-dbgsym_1.3.0-1_armel.deb 2507100a2eec0adda2590a0be2699c3119b5036c3c1c7b18a02766772896858f 4668 kma_1.3.0-1_armel.buildinfo 92a7e425461b2aa324d3ac80da5fba5ae8b340145129b100d61d18e5b9871614 121704 kma_1.3.0-1_armel.deb Files: 6749a36228ba48e96cc6c43a34b92b10 386400 debug optional kma-dbgsym_1.3.0-1_armel.deb 46bac9bf8def4c4d9ab2559d9870afaf 4668 science optional kma_1.3.0-1_armel.buildinfo 9938e357b85f9ac8cb25e54f9a4c9c36 121704 science optional kma_1.3.0-1_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: kma Binary: kma kma-dbgsym Architecture: armel Version: 1.3.0-1 Checksums-Md5: 6749a36228ba48e96cc6c43a34b92b10 386400 kma-dbgsym_1.3.0-1_armel.deb 9938e357b85f9ac8cb25e54f9a4c9c36 121704 kma_1.3.0-1_armel.deb Checksums-Sha1: 995136a2c89dabbfe82f4efa2d559e82635d9433 386400 kma-dbgsym_1.3.0-1_armel.deb 40c3c8dedf8e7705f3a0244585aa8ce139b9695b 121704 kma_1.3.0-1_armel.deb Checksums-Sha256: 7a80010d08449b6a8a37bb3dc5ed2bacdaadaa1951a00528814d4e390a1b0cbb 386400 kma-dbgsym_1.3.0-1_armel.deb 92a7e425461b2aa324d3ac80da5fba5ae8b340145129b100d61d18e5b9871614 121704 kma_1.3.0-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 06 Jul 2020 10:08:55 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-3), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-6), binutils (= 2.34-8), binutils-common (= 2.34-8), binutils-x86-64-linux-gnu (= 2.34-8), bsdextrautils (= 2.35.2-6), bsdutils (= 1:2.35.2-6), build-essential (= 12.8), bzip2 (= 1.0.8-3), coreutils (= 8.32-2), cpp (= 4:9.2.1-3.1), cpp-9 (= 9.3.0-14), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2), debianutils (= 4.11), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.8.1-2), diffutils (= 1:3.7-3), dmsetup (= 2:1.02.167-1+b1), dpkg (= 1.20.3), dpkg-dev (= 1.20.3), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.3.0-14), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10.1.0-4), gcc-9 (= 9.3.0-14), gcc-9-base (= 9.3.0-14), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), hostname (= 3.23), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20171227-0.2), libasan5 (= 9.3.0-14), libatomic1 (= 10.1.0-4), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbinutils (= 2.34-8), libblkid1 (= 2.35.2-6), libbz2-1.0 (= 1.0.8-3), libc-bin (= 2.30-8), libc-dev-bin (= 2.30-8), libc6 (= 2.30-8), libc6-dev (= 2.30-8), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.1.0-4), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1), libcrypt1 (= 1:4.4.16-1), libcryptsetup12 (= 2:2.3.3-1), libctf-nobfd0 (= 2.34-8), libctf0 (= 2.34-8), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.253), libdebhelper-perl (= 13.2), libdevmapper1.02.1 (= 2:1.02.167-1+b1), libdpkg-perl (= 1.20.3), libelf1 (= 0.176-1.1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.8.1-2), libgcc-9-dev (= 9.3.0-14), libgcc-s1 (= 10.1.0-4), libgcrypt20 (= 1.8.5-5), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.3-2), libgmp10 (= 2:6.2.0+dfsg-6), libgomp1 (= 10.1.0-4), libgpg-error0 (= 1.38-2), libicu67 (= 67.1-2), libisl22 (= 0.22.1-1), libitm1 (= 10.1.0-4), libjson-c4 (= 0.13.1+dfsg-9), liblsan0 (= 10.1.0-4), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.35.2-6), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), 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 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.2-2), libquadmath0 (= 10.1.0-4), libseccomp2 (= 2.4.3-1+b1), libselinux1 (= 3.0-1+b3), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.35.2-6), libssl1.1 (= 1.1.1g-1), libstdc++-9-dev (= 9.3.0-14), libstdc++6 (= 10.1.0-4), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.6-2), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libtsan0 (= 10.1.0-4), libubsan1 (= 10.1.0-4), libuchardet0 (= 0.0.7-1), libudev1 (= 245.6-2), libunistring2 (= 0.9.10-4), libuuid1 (= 2.35.2-6), libxml2 (= 2.9.10+dfsg-5+b1), linux-libc-dev (= 5.7.6-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.3-4), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-3), tar (= 1.30+dfsg-7), util-linux (= 2.35.2-6), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) 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="1593952279" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ kma-dbgsym_1.3.0-1_armel.deb ---------------------------- new Debian package, version 2.0. size 386400 bytes: control archive=692 bytes. 436 bytes, 12 lines control 399 bytes, 4 lines md5sums Package: kma-dbgsym Source: kma Version: 1.3.0-1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 426 Depends: kma (= 1.3.0-1) Section: debug Priority: optional Description: debug symbols for kma Build-Ids: 04845f42a28b81f2f9455224eb7797d1c372c866 3d44e95d5939619903d6790f5a10b1113f5cb087 c24e8e765e4c890929a8faa4682762580e9c3c94 drwxr-xr-x root/root 0 2020-07-05 12:31 ./ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.build-id/04/ -rw-r--r-- root/root 388196 2020-07-05 12:31 ./usr/lib/debug/.build-id/04/845f42a28b81f2f9455224eb7797d1c372c866.debug drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.build-id/3d/ -rw-r--r-- root/root 8028 2020-07-05 12:31 ./usr/lib/debug/.build-id/3d/44e95d5939619903d6790f5a10b1113f5cb087.debug drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.build-id/c2/ -rw-r--r-- root/root 19900 2020-07-05 12:31 ./usr/lib/debug/.build-id/c2/4e8e765e4c890929a8faa4682762580e9c3c94.debug drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/lib/debug/.dwz/arm-linux-gnueabi/ -rw-r--r-- root/root 3908 2020-07-05 12:31 ./usr/lib/debug/.dwz/arm-linux-gnueabi/kma.debug drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-07-05 12:31 ./usr/share/doc/kma-dbgsym -> kma kma_1.3.0-1_armel.deb --------------------- new Debian package, version 2.0. size 121704 bytes: control archive=1068 bytes. 882 bytes, 17 lines control 543 bytes, 9 lines md5sums Package: kma Version: 1.3.0-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 332 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 2020-07-05 12:31 ./ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/bin/ -rwxr-xr-x root/root 300692 2020-07-05 12:31 ./usr/bin/kma -rwxr-xr-x root/root 5660 2020-07-05 12:31 ./usr/bin/kma_index -rwxr-xr-x root/root 13852 2020-07-05 12:31 ./usr/bin/kma_shm drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/doc/kma/ -rw-r--r-- root/root 2947 2020-07-01 11:31 ./usr/share/doc/kma/README.md.gz -rw-r--r-- root/root 596 2020-07-05 12:31 ./usr/share/doc/kma/changelog.Debian.gz -rw-r--r-- root/root 952 2020-07-05 12:31 ./usr/share/doc/kma/copyright drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-05 12:31 ./usr/share/man/man1/ -rw-r--r-- root/root 1312 2020-07-05 12:31 ./usr/share/man/man1/kma.1.gz -rw-r--r-- root/root 697 2020-07-05 12:31 ./usr/share/man/man1/kma_index.1.gz -rw-r--r-- root/root 426 2020-07-05 12:31 ./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 [629 B] Fetched 2131 B in 0s (99.0 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-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdynaloader-functions-perl libemail-address-xs-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmetrics-any-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtest-metrics-any-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian patchutils readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl 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 libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libpackage-stash-xs-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-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdynaloader-functions-perl libemail-address-xs-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl libmetrics-any-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtest-metrics-any-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian patchutils readline-common sbuild-build-depends-lintian-dummy:armel t1utils 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 6807 kB of archives. After this operation, 19.2 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7.1 [50.5 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.32.3-1 [753 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-3+b5 [38.4 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.45-1 [15.1 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-tiny-perl all 2.24-1 [16.2 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.19-1 [126 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libdata-validate-domain-perl all 0.10-1 [12.3 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-size-perl amd64 0.83-1+b1 [26.0 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-address-xs-perl amd64 1.04-1+b2 [28.1 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.11-1 [8888 B] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libfont-ttf-perl all 1.06-1 [317 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.45-1 [84.4 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-5 [105 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.12-1 [12.9 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libmetrics-any-perl all 0.05-2 [36.8 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libtest-metrics-any-perl all 0.01-2 [7060 B] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.77-3 [274 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.017-1 [16.8 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.21-1 [12.1 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libjson-maybexs-perl all 1.004002-1 [13.1 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.004000-1 [59.4 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.114-1 [53.6 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.014+ds-1 [106 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.014+ds-1 [108 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-1 [39.2 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010002-1 [338 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-3 [89.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.82.0 [1293 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6807 kB in 0s (31.0 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20097 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.3-7.1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7.1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../04-gpgconf_2.2.20-1_amd64.deb ... Unpacking gpgconf (2.2.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../05-libsqlite3-0_3.32.3-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.32.3-1) ... Selecting previously unselected package gpg. Preparing to unpack .../06-gpg_2.2.20-1_amd64.deb ... Unpacking gpg (2.2.20-1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../07-libapt-pkg-perl_0.1.36+b3_amd64.deb ... Unpacking libapt-pkg-perl (0.1.36+b3) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../08-libb-hooks-op-check-perl_0.22-1+b2_amd64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../09-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../10-libdevel-callchecker-perl_0.008-1+b1_amd64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../11-libparams-classify-perl_0.015-1+b2_amd64.deb ... 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Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../17-libb-hooks-endofscope-perl_0.24-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.24-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../18-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../19-libclass-method-modifiers-perl_2.13-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.13-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../20-libclass-xsaccessor-perl_1.19-3+b5_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-3+b5) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../21-libclone-perl_0.45-1_amd64.deb ... Unpacking libclone-perl (0.45-1) ... Selecting previously unselected package libconfig-tiny-perl. 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Unpacking sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.36+b3) ... Setting up libunicode-utf8-perl (0.62-1+b1) ... Setting up libstruct-dumb-perl (0.12-1) ... Setting up libdynaloader-functions-perl (0.003-1) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up liblist-compare-perl (0.53-1) ... Setting up libclone-perl (0.45-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libsub-identify-perl (0.14-1+b2) ... Setting up libcpanel-json-xs-perl (4.19-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdevel-size-perl (0.83-1+b1) ... Setting up libsqlite3-0:amd64 (3.32.3-1) ... Setting up libfuture-perl (0.45-1) ... Setting up libyaml-libyaml-perl (0.82+repack-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libtext-levenshtein-perl (0.13-1) ... Setting up libassuan0:amd64 (2.5.3-7.1) ... Setting up libconfig-tiny-perl (2.24-1) ... 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 8912 Build-Time: 22 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 18 Job: kma_1.3.0-1 Lintian: pass Machine Architecture: amd64 Package: kma Package-Time: 49 Source-Version: 1.3.0-1 Space: 8912 Status: successful Version: 1.3.0-1 -------------------------------------------------------------------------------- Finished at 2020-07-06T10:08:55Z Build needed 00:00:49, 8912k disk space