sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | idba 1.1.3-7 (s390x) Tue, 02 Jun 2020 11:47:05 +0000 | +==============================================================================+ Package: idba Version: 1.1.3-7 Source Version: 1.1.3-7 Distribution: unstable Machine Architecture: amd64 Host Architecture: s390x Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-b8bffcbd-eb2a-494b-b364-6575ec7b716f' with '<>' I: NOTICE: Log filtering will replace 'build/idba-l1UChj/resolver-4mUwSa' 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 2020-06-02-0802.20.pdiff [11.5 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-06-02-0802.20.pdiff [11.5 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-02-0802.20.pdiff [9380 B] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-06-02-0802.20.pdiff [9380 B] Get:6 http://debian.oregonstate.edu/debian unstable/main s390x Packages [7902 kB] Fetched 8125 kB in 2s (5376 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libunistring2 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 379 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 libunistring2 amd64 0.9.10-4 [379 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 379 kB in 0s (7322 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10323 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-4_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-4) over (0.9.10-3) ... Setting up libunistring2:amd64 (0.9.10-4) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'idba' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/idba.git Please use: git clone https://salsa.debian.org/med-team/idba.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 711 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main idba 1.1.3-7 (dsc) [2022 B] Get:2 http://debian.oregonstate.edu/debian unstable/main idba 1.1.3-7 (tar) [446 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main idba 1.1.3-7 (diff) [263 kB] Fetched 711 kB in 0s (8558 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/idba-l1UChj/idba-1.1.3' with '<>' I: NOTICE: Log filtering will replace 'build/idba-l1UChj' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64, libc-dev:s390x, libstdc++-dev:s390x Filtered Build-Depends: debhelper-compat (= 12), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64, libc-dev:s390x, libstdc++-dev:s390x 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 [428 B] Get:5 copy:/<>/apt_archive ./ Packages [493 B] Fetched 1878 B in 0s (73.2 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-s390x-linux-gnu bsdmainutils build-essential cpp-9-s390x-linux-gnu cpp-s390x-linux-gnu cross-config crossbuild-essential-s390x debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-s390x-linux-gnu g++-s390x-linux-gnu gcc-10-base:s390x gcc-10-cross-base gcc-9-base:s390x gcc-9-cross-base gcc-9-s390x-linux-gnu gcc-9-s390x-linux-gnu-base gcc-s390x-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:s390x libasan5-s390x-cross libatomic1:s390x libatomic1-s390x-cross libbsd0 libc6:s390x libc6-dev libc6-dev:s390x libc6-dev-s390x-cross libc6-s390x-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:s390x libcrypt1:s390x libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:s390x libgcc-9-dev-s390x-cross libgcc-s1:s390x libgcc-s1-s390x-cross libglib2.0-0 libgomp1:s390x libgomp1-s390x-cross libicu63 libio-string-perl libitm1:s390x libitm1-s390x-cross liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:s390x libstdc++-9-dev-s390x-cross libstdc++6:s390x libstdc++6-s390x-cross libsub-override-perl libtool libubsan1:s390x libubsan1-s390x-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:s390x linux-libc-dev-s390x-cross m4 man-db perl perl-modules-5.30 po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-9-multilib gcc-9-doc g++-9-multilib-s390x-linux-gnu gcc-9-multilib-s390x-linux-gnu manpages-dev flex bison gdb-s390x-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:s390x libc-l10n:s390x locales:s390x glibc-doc manpages-dev:s390x gnupg | gnupg2 git bzr libstdc++-9-doc libstdc++-9-doc:s390x 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 libb-debug-perl liblocale-codes-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: gnupg | gnupg2 libalgorithm-merge-perl curl | wget | lynx libidn2-0:s390x 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-s390x-linux-gnu bsdmainutils build-essential cpp-9-s390x-linux-gnu cpp-s390x-linux-gnu cross-config crossbuild-essential-s390x debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-9 g++-9-s390x-linux-gnu g++-s390x-linux-gnu gcc-10-base:s390x gcc-10-cross-base gcc-9-base:s390x gcc-9-cross-base gcc-9-s390x-linux-gnu gcc-9-s390x-linux-gnu-base gcc-s390x-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:s390x libasan5-s390x-cross libatomic1:s390x libatomic1-s390x-cross libbsd0 libc6:s390x libc6-dev libc6-dev:s390x libc6-dev-s390x-cross libc6-s390x-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:s390x libcrypt1:s390x libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:s390x libgcc-9-dev-s390x-cross libgcc-s1:s390x libgcc-s1-s390x-cross libglib2.0-0 libgomp1:s390x libgomp1-s390x-cross libicu63 libio-string-perl libitm1:s390x libitm1-s390x-cross liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-9-dev libstdc++-9-dev:s390x libstdc++-9-dev-s390x-cross libstdc++6:s390x libstdc++6-s390x-cross libsub-override-perl libtool libubsan1:s390x libubsan1-s390x-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:s390x linux-libc-dev-s390x-cross m4 man-db perl perl-modules-5.30 po-debconf sbuild-build-depends-main-dummy:s390x sensible-utils ucf 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 85.5 MB of archives. After this operation, 361 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.2-1 [1315 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-1 [2807 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-1 [4011 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-1 [290 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main s390x gcc-10-base s390x 10.1.0-3 [197 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main s390x gcc-9-base s390x 9.3.0-13 [197 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0042 [73.9 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-1 [775 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-s390x-linux-gnu amd64 2.34-8 [1946 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-8 [2631 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-13 [1701 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-13 [10.7 MB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.19.7 [1414 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.19.7 [1773 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-s390x-linux-gnu-base amd64 9.3.0-13cross1 [197 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-s390x-linux-gnu amd64 9.3.0-13cross1 [6145 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-s390x-linux-gnu amd64 4:9.2.1-3.1 [16.7 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-13cross1 [193 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.1.0-3cross1 [194 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-s390x-cross all 2.30-2cross1 [1246 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-s390x-cross all 10.1.0-3cross1 [24.7 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-s390x-cross all 10.1.0-3cross1 [90.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-s390x-cross all 10.1.0-3cross1 [24.9 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-s390x-cross all 10.1.0-3cross1 [7940 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-s390x-cross all 9.3.0-13cross1 [338 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-s390x-cross all 10.1.0-3cross1 [440 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-s390x-cross all 10.1.0-3cross1 [125 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-s390x-cross all 9.3.0-13cross1 [681 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-s390x-linux-gnu amd64 9.3.0-13cross1 [6529 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-s390x-linux-gnu amd64 4:9.2.1-3.1 [1456 B] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-s390x-cross all 5.4.19-1cross1 [1173 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-s390x-cross all 2.30-2cross1 [2207 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-s390x-cross all 9.3.0-13cross1 [1652 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-s390x-linux-gnu amd64 9.3.0-13cross1 [6729 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 g++-s390x-linux-gnu amd64 4:9.2.1-3.1 [1176 B] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-s390x all 12.8 [6636 B] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.1 [187 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.1-1 [14.9 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.3-1 [1341 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.1 [1012 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main s390x libgcc-s1 s390x 10.1.0-3 [24.6 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main s390x libcrypt1 s390x 1:4.4.16-1 [89.0 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main s390x libc6 s390x 2.30-8 [2465 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main s390x libasan5 s390x 9.3.0-13 [344 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main s390x libatomic1 s390x 10.1.0-3 [8104 B] Get:93 http://debian.oregonstate.edu/debian unstable/main s390x linux-libc-dev s390x 5.6.14-1 [1113 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main s390x libcrypt-dev s390x 1:4.4.16-1 [107 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main s390x libc6-dev s390x 2.30-8 [2237 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main s390x libgomp1 s390x 10.1.0-3 [92.0 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main s390x libitm1 s390x 10.1.0-3 [25.3 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main s390x libstdc++6 s390x 10.1.0-3 [483 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main s390x libubsan1 s390x 10.1.0-3 [125 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main s390x libgcc-9-dev s390x 9.3.0-13 [681 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main s390x libstdc++-9-dev s390x 9.3.0-13 [1664 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.5 MB in 1s (117 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 10323 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.2-1_amd64.deb ... Unpacking man-db (2.9.2-1) ... 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Setting up libgomp1-s390x-cross (10.1.0-3cross1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:s390x (9.3.0-13) ... Setting up libstdc++-9-dev:amd64 (9.3.0-13) ... Setting up cpp-s390x-linux-gnu (4:9.2.1-3.1) ... Setting up libtool (2.4.6-14) ... Setting up libatomic1-s390x-cross (10.1.0-3cross1) ... Setting up m4 (1.4.18-4) ... Setting up perl (5.30.3-1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libgcc-s1-s390x-cross (10.1.0-3cross1) ... Setting up ucf (3.0042) ... Setting up g++-9 (9.3.0-13) ... Setting up libdpkg-perl (1.19.7) ... 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 (1:1.16.2-1) ... 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 libstdc++6-s390x-cross (10.1.0-3cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up libasan5-s390x-cross (9.3.0-13cross1) ... Setting up man-db (2.9.2-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.19.7) ... 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 build-essential (12.8) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libubsan1-s390x-cross (10.1.0-3cross1) ... 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 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 (1.8.1-1) ... Setting up libgcc-9-dev-s390x-cross (9.3.0-13cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libstdc++-9-dev-s390x-cross (9.3.0-13cross1) ... Setting up gcc-9-s390x-linux-gnu (9.3.0-13cross1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up gcc-s390x-linux-gnu (4:9.2.1-3.1) ... Setting up g++-9-s390x-linux-gnu (9.3.0-13cross1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up g++-s390x-linux-gnu (4:9.2.1-3.1) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-s390x (12.8) ... Setting up libcrypt1:s390x (1:4.4.16-1) ... Setting up libgcc-s1:s390x (10.1.0-3) ... Setting up libc6:s390x (2.30-8) ... Setting up libcrypt-dev:s390x (1:4.4.16-1) ... Setting up libc6-dev:s390x (2.30-8) ... Setting up libstdc++6:s390x (10.1.0-3) ... Setting up libitm1:s390x (10.1.0-3) ... Setting up debhelper (13.1) ... Setting up libgomp1:s390x (10.1.0-3) ... Setting up dh-autoreconf (19) ... Setting up libasan5:s390x (9.3.0-13) ... Setting up libatomic1:s390x (10.1.0-3) ... Setting up libubsan1:s390x (10.1.0-3) ... Setting up libgcc-9-dev:s390x (9.3.0-13) ... Setting up libstdc++-9-dev:s390x (9.3.0-13) ... Setting up sbuild-build-depends-main-dummy:s390x (0.invalid.0) ... Processing triggers for libc-bin (2.30-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x 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_1.19.7 g++-9_9.3.0-13 gcc-9_9.3.0-13 libc6-dev_2.30-8 libstdc++-9-dev_9.3.0-13 libstdc++-9-dev-s390x-cross_9.3.0-13cross1 libstdc++6_10.1.0-3 libstdc++6-s390x-cross_10.1.0-3cross1 linux-libc-dev_5.6.14-1 Package versions: adduser_3.118 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1 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-s390x-linux-gnu_2.34-8 binutils-x86-64-linux-gnu_2.34-8 bsdmainutils_11.1.2+b1 bsdutils_1:2.35.2-2 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.4.0-4 cpp-9_9.3.0-13 cpp-9-s390x-linux-gnu_9.3.0-13cross1 cpp-s390x-linux-gnu_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-s390x_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debian-archive-keyring_2019.1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-2 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-13 g++-9-s390x-linux-gnu_9.3.0-13cross1 g++-s390x-linux-gnu_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10.1.0-3 gcc-10-cross-base_10.1.0-3cross1 gcc-8-base_8.4.0-4 gcc-9_9.3.0-13 gcc-9-base_9.3.0-13 gcc-9-cross-base_9.3.0-13cross1 gcc-9-s390x-linux-gnu_9.3.0-13cross1 gcc-9-s390x-linux-gnu-base_9.3.0-13cross1 gcc-s390x-linux-gnu_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.5 libarchive-zip-perl_1.68-1 libasan5_9.3.0-13 libasan5-s390x-cross_9.3.0-13cross1 libatomic1_10.1.0-3 libatomic1-s390x-cross_10.1.0-3cross1 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_2.35.2-2 libbsd0_0.10.0-1 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 libc6-dev-s390x-cross_2.30-2cross1 libc6-s390x-cross_2.30-2cross1 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10.1.0-3 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000003-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8 libctf0_2.34-8 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-2 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.8.1-1 libfile-which-perl_1.23-1 libgcc-9-dev_9.3.0-13 libgcc-9-dev-s390x-cross_9.3.0-13cross1 libgcc-s1_10.1.0-3 libgcc-s1-s390x-cross_10.1.0-3cross1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-4 libgomp1_10.1.0-3 libgomp1-s390x-cross_10.1.0-3cross1 libgpg-error0_1.37-1 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.1.0-3 libitm1-s390x-cross_10.1.0-3cross1 liblocale-gettext-perl_1.07-4 liblsan0_10.1.0-3 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.4.0-4 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 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_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.3-1 libpipeline1_1.5.2-2 libquadmath0_10.1.0-3 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-2 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-13 libstdc++-9-dev-s390x-cross_9.3.0-13cross1 libstdc++6_10.1.0-3 libstdc++6-s390x-cross_10.1.0-3cross1 libsub-override-perl_0.09-2 libsystemd0_245.5-3 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10.1.0-3 libubsan1_10.1.0-3 libubsan1-s390x-cross_10.1.0-3cross1 libuchardet0_0.0.7-1 libudev1_245.5-3 libunistring2_0.9.10-4 libuuid1_2.35.2-2 libxml-libxml-perl_2.0134+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-5 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.14-1 linux-libc-dev-s390x-cross_5.4.19-1cross1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-1 man-db_2.9.2-1 mawk_1.3.4.20200120-2 mount_2.35.2-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-1 perl-base_5.30.3-1 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.3-1 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0042 util-linux_2.35.2-2 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: idba Binary: idba, idba-extra Architecture: any Version: 1.1.3-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/loneknightpy/idba Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/idba Vcs-Git: https://salsa.debian.org/med-team/idba.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), libgtest-dev , python3 Package-List: idba deb science optional arch=any idba-extra deb science optional arch=any Checksums-Sha1: cf673154a9696215648177f0bc43b9cc25feaf26 446227 idba_1.1.3.orig.tar.gz 359f30b05dc8923891739df705e636c461ad3e89 263052 idba_1.1.3-7.debian.tar.xz Checksums-Sha256: 030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0 446227 idba_1.1.3.orig.tar.gz 540627574366ca2cbb36bed35fcc988d74418d95aae1b23676ecd73e6d632c84 263052 idba_1.1.3-7.debian.tar.xz Files: 41fe7eabdcfaea677558f3e4baeb2ea8 446227 idba_1.1.3.orig.tar.gz 2be67984af689e298100b910d25d62c1 263052 idba_1.1.3-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6angURHHRpbGxlQGRl 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F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./idba_1.1.3-7.dsc dpkg-source: info: extracting idba in /<> dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz dpkg-source: info: unpacking idba_1.1.3-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install_all_idba_flavours.patch dpkg-source: info: applying use-atomic-for-mips.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying use_debian_packaged_googletest.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.s390x 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-b8bffcbd-eb2a-494b-b364-6575ec7b716f SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -as390x -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package idba dpkg-buildpackage: info: source version 1.1.3-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type s390x-linux-gnu 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 s390x debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation bin/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') bin/Makefile.am:9: warning: source file '$(top_srcdir)/src/tools/fa2fq.cpp' is in a subdirectory, bin/Makefile.am:9: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. bin/Makefile.am:19: warning: source file '$(top_srcdir)/src/tools/filter_blat.cpp' is in a subdirectory, bin/Makefile.am:19: but option 'subdir-objects' is disabled bin/Makefile.am:17: warning: source file '$(top_srcdir)/src/tools/filter_contigs.cpp' is in a subdirectory, bin/Makefile.am:17: but option 'subdir-objects' is disabled bin/Makefile.am:33: warning: source file '$(top_srcdir)/src/release/filterfa.cpp' is in a subdirectory, bin/Makefile.am:33: but option 'subdir-objects' is disabled bin/Makefile.am:25: warning: source file '$(top_srcdir)/src/release/fq2fa.cpp' is in a subdirectory, bin/Makefile.am:25: but option 'subdir-objects' is disabled bin/Makefile.am:34: warning: source file '$(top_srcdir)/src/release/idba.cpp' is in a subdirectory, bin/Makefile.am:34: but option 'subdir-objects' is disabled bin/Makefile.am:30: warning: source file '$(top_srcdir)/src/release/idba_hybrid.cpp' is in a subdirectory, bin/Makefile.am:30: but option 'subdir-objects' is disabled bin/Makefile.am:29: warning: source file '$(top_srcdir)/src/release/idba_tran.cpp' is in a subdirectory, bin/Makefile.am:29: but option 'subdir-objects' is disabled bin/Makefile.am:13: warning: source file '$(top_srcdir)/src/tools/idba_tran_test.cpp' is in a subdirectory, bin/Makefile.am:13: but option 'subdir-objects' is disabled bin/Makefile.am:27: warning: source file '$(top_srcdir)/src/release/idba_ud.cpp' is in a subdirectory, bin/Makefile.am:27: but option 'subdir-objects' is disabled bin/Makefile.am:31: warning: source file '$(top_srcdir)/src/release/parallel_blat.cpp' is in a subdirectory, bin/Makefile.am:31: but option 'subdir-objects' is disabled bin/Makefile.am:18: warning: source file '$(top_srcdir)/src/tools/parallel_rna_blat.cpp' is in a subdirectory, bin/Makefile.am:18: but option 'subdir-objects' is disabled bin/Makefile.am:12: warning: source file '$(top_srcdir)/src/tools/print_graph.cpp' is in a subdirectory, bin/Makefile.am:12: but option 'subdir-objects' is disabled bin/Makefile.am:28: warning: source file '$(top_srcdir)/src/release/raw_n50.cpp' is in a subdirectory, bin/Makefile.am:28: but option 'subdir-objects' is disabled bin/Makefile.am:14: warning: source file '$(top_srcdir)/src/tools/sample_reads.cpp' is in a subdirectory, bin/Makefile.am:14: but option 'subdir-objects' is disabled bin/Makefile.am:7: warning: source file '$(top_srcdir)/src/tools/scaffold.cpp' is in a subdirectory, bin/Makefile.am:7: but option 'subdir-objects' is disabled bin/Makefile.am:6: warning: source file '$(top_srcdir)/src/tools/shuffle_reads.cpp' is in a subdirectory, bin/Makefile.am:6: but option 'subdir-objects' is disabled bin/Makefile.am:36: warning: source file '$(top_srcdir)/src/release/sim_reads.cpp' is in a subdirectory, bin/Makefile.am:36: but option 'subdir-objects' is disabled bin/Makefile.am:32: warning: source file '$(top_srcdir)/src/release/sim_reads_tran.cpp' is in a subdirectory, bin/Makefile.am:32: but option 'subdir-objects' is disabled bin/Makefile.am:15: warning: source file '$(top_srcdir)/src/tools/sort_psl.cpp' is in a subdirectory, bin/Makefile.am:15: but option 'subdir-objects' is disabled bin/Makefile.am:16: warning: source file '$(top_srcdir)/src/tools/sort_reads.cpp' is in a subdirectory, bin/Makefile.am:16: but option 'subdir-objects' is disabled bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory, bin/Makefile.am:20: but option 'subdir-objects' is disabled bin/Makefile.am:23: warning: source file '$(top_srcdir)/src/tools/split_fq.cpp' is in a subdirectory, bin/Makefile.am:23: but option 'subdir-objects' is disabled bin/Makefile.am:35: warning: source file '$(top_srcdir)/src/release/split_scaffold.cpp' is in a subdirectory, bin/Makefile.am:35: but option 'subdir-objects' is disabled bin/Makefile.am:21: warning: source file '$(top_srcdir)/src/tools/test.cpp' is in a subdirectory, bin/Makefile.am:21: but option 'subdir-objects' is disabled bin/Makefile.am:8: warning: source file '$(top_srcdir)/src/tools/validate_component.cpp' is in a subdirectory, bin/Makefile.am:8: but option 'subdir-objects' is disabled bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory, bin/Makefile.am:26: but option 'subdir-objects' is disabled bin/Makefile.am:11: warning: source file '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' is in a subdirectory, bin/Makefile.am:11: but option 'subdir-objects' is disabled bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory, bin/Makefile.am:22: but option 'subdir-objects' is disabled bin/Makefile.am:10: warning: source file '$(top_srcdir)/src/tools/validate_rna.cpp' is in a subdirectory, bin/Makefile.am:10: but option 'subdir-objects' is disabled lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/hash_aligner.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/options_description.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/blat_record.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_reader.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/compact_sequence.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph_branch_group.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/scaffold_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph_branch_group.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_info.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/local_assembler.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/assembly_utility.cpp' is in a subdirectory, lib/Makefile.am:5: but option 'subdir-objects' is disabled lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, lib/Makefile.am:68: but option 'subdir-objects' is disabled lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest-all.cc' is in a subdirectory, lib/Makefile.am:68: but option 'subdir-objects' is disabled test/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') test/Makefile.am:11: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:11: but option 'subdir-objects' is disabled test/Makefile.am:11: warning: source file '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' is in a subdirectory, test/Makefile.am:11: but option 'subdir-objects' is disabled test/Makefile.am:8: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:8: but option 'subdir-objects' is disabled test/Makefile.am:8: warning: source file '$(top_srcdir)/src/test/bit_edges_unittest.cpp' is in a subdirectory, test/Makefile.am:8: but option 'subdir-objects' is disabled test/Makefile.am:6: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:6: but option 'subdir-objects' is disabled test/Makefile.am:6: warning: source file '$(top_srcdir)/src/test/compact_sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:6: but option 'subdir-objects' is disabled test/Makefile.am:17: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:17: but option 'subdir-objects' is disabled test/Makefile.am:17: warning: source file '$(top_srcdir)/src/test/hash_map_unittest.cpp' is in a subdirectory, test/Makefile.am:17: but option 'subdir-objects' is disabled test/Makefile.am:10: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:10: but option 'subdir-objects' is disabled test/Makefile.am:10: warning: source file '$(top_srcdir)/src/test/hash_set_unittest.cpp' is in a subdirectory, test/Makefile.am:10: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/test/hash_table_unittest.cpp' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:13: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:13: but option 'subdir-objects' is disabled test/Makefile.am:13: warning: source file '$(top_srcdir)/src/test/histgram_unittest.cpp' is in a subdirectory, test/Makefile.am:13: but option 'subdir-objects' is disabled test/Makefile.am:9: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:9: but option 'subdir-objects' is disabled test/Makefile.am:9: warning: source file '$(top_srcdir)/src/test/kmer_unittest.cpp' is in a subdirectory, test/Makefile.am:9: but option 'subdir-objects' is disabled test/Makefile.am:14: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:14: but option 'subdir-objects' is disabled test/Makefile.am:14: warning: source file '$(top_srcdir)/src/test/managed_list_unittest.cpp' is in a subdirectory, test/Makefile.am:14: but option 'subdir-objects' is disabled test/Makefile.am:15: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:15: but option 'subdir-objects' is disabled test/Makefile.am:15: warning: source file '$(top_srcdir)/src/test/sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:15: but option 'subdir-objects' is disabled test/Makefile.am:16: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:16: but option 'subdir-objects' is disabled test/Makefile.am:16: warning: source file '$(top_srcdir)/src/test/short_sequence_unittest.cpp' is in a subdirectory, test/Makefile.am:16: but option 'subdir-objects' is disabled test/Makefile.am:12: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory, test/Makefile.am:12: but option 'subdir-objects' is disabled test/Makefile.am:12: warning: source file '$(top_srcdir)/src/test/vertex_status_unittest.cpp' is in a subdirectory, test/Makefile.am:12: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" LIBS=" -latomic" ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=s390x-linux-gnu "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" "LIBS= -latomic" configure: loading site script /etc/dpkg-cross/cross-config.s390x checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for s390x-linux-gnu-strip... s390x-linux-gnu-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for s390x-linux-gnu-g++... s390x-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether s390x-linux-gnu-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of s390x-linux-gnu-g++... none checking for s390x-linux-gnu-gcc... s390x-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether s390x-linux-gnu-gcc accepts -g... yes checking for s390x-linux-gnu-gcc option to accept ISO C89... none needed checking whether s390x-linux-gnu-gcc understands -c and -o together... yes checking dependency style of s390x-linux-gnu-gcc... none checking for s390x-linux-gnu-ranlib... s390x-linux-gnu-ranlib checking how to run the C preprocessor... s390x-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for working memcmp... no checking for vprintf... yes checking for _doprnt... no checking for sqrt... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating lib/Makefile config.status: creating test/Makefile config.status: creating script/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' dh_auto_build -a make -j1 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in lib make[3]: Entering directory '/<>/lib' s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp ../src/misc/log.cpp: In destructor ‘LogProcess::~LogProcess()’: ../src/misc/log.cpp:78:58: warning: throw will always call terminate() [-Wterminate] 78 | throw runtime_error("cannot kill log process"); | ^ ../src/misc/log.cpp:78:58: note: in C++11 destructors default to noexcept ../src/misc/log.cpp: In static member function ‘static void* LogThread::LogThreadFunc(void*)’: ../src/misc/log.cpp:122:14: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] 122 | write(log_thread.out_fd, line, len); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp ../src/graph/contig_graph.cpp: In member function ‘void ContigGraph::TopSort(std::deque&, std::deque&)’: ../src/graph/contig_graph.cpp:1391:30: warning: variable ‘end’ set but not used [-Wunused-but-set-variable] 1391 | ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component); | ^~~ s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp ../src/assembly/local_assembler.cpp: In static member function ‘static void* LocalAssemblerWithReference::LocalAssembleThread(void*)’: ../src/assembly/local_assembler.cpp:488:22: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable] 488 | bool flag = false; | ^~~~ ../src/assembly/local_assembler.cpp:489:21: warning: variable ‘aligned’ set but not used [-Wunused-but-set-variable] 489 | int aligned[2] = {0}; | ^~~~~~~ s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp rm -f libassembly.a ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o ar: `u' modifier ignored since `D' is the default (see `U') s390x-linux-gnu-ranlib libassembly.a s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc In file included from /usr/s390x-linux-gnu/include/string.h:495, from ../gtest_src/gtest/gtest.h:285, from ../gtest_src/gtest/gtest-all.cc:39: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘const char* testing::internal::posix::StrNCpy(char*, const char*, size_t)’ at ../gtest_src/gtest/gtest.h:2672:17, inlined from ‘char* testing::internal::CloneString(const char*, size_t)’ at ../gtest_src/gtest/gtest-all.cc:2144:19, inlined from ‘static const char* testing::internal::String::CloneCString(const char*)’ at ../gtest_src/gtest/gtest-all.cc:2155:39: /usr/s390x-linux-gnu/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../gtest_src/gtest/gtest-all.cc: In static member function ‘static const char* testing::internal::String::CloneCString(const char*)’: ../gtest_src/gtest/gtest-all.cc:2155:39: note: length computed here 2155 | NULL : CloneString(c_str, strlen(c_str)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f libgtest.a ar cru libgtest.a gtest_main.o gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') s390x-linux-gnu-ranlib libgtest.a make[3]: Leaving directory '/<>/lib' Making all in bin make[3]: Entering directory '/<>/bin' s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp ../src/release/idba_tran.cpp: In function ‘void FindIsoforms(ContigGraphPath&, std::deque&, ContigGraph&, std::deque&)’: ../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 241 | if (flag && path.size() > option.min_transcript) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/release/idba_tran.cpp: In function ‘void Assemble(HashGraph&)’: ../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 523 | if (transcripts[i].size() >= option.min_transcript) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp ../src/tools/validate_component.cpp: In function ‘int main(int, char**)’: ../src/tools/validate_component.cpp:141:13: warning: unused variable ‘ref_id’ [-Wunused-variable] 141 | int ref_id = dict[record.ref_name]; | ^~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp ../src/tools/validate_rna.cpp: In function ‘int main(int, char**)’: ../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 396 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp ../src/tools/validate_contigs_mummer.cpp: In function ‘int main(int, char**)’: ../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 218 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 219 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 220 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 221 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] 222 | fgets(line, MaxLine, fcoord); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp ../src/tools/parallel_rna_blat.cpp: In function ‘void CreateFile(const string&)’: ../src/tools/parallel_rna_blat.cpp:47:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 47 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function ‘void RemoveFile(const string&)’: ../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 53 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function ‘void Append(const string&, const string&)’: ../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 59 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/tools/parallel_rna_blat.cpp: In function ‘void RunBlat(const string&)’: ../src/tools/parallel_rna_blat.cpp:96:19: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 96 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp ../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive 6 | #include "graph/contig_graph.h"; | ^ ../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive 7 | #include "sequence/sequence.h"; | ^ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp ../src/release/validate_contigs_blat.cpp: In function ‘int main(int, char**)’: ../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 388 | fscanf(flist, "%s %lf", buf, &coverage[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp ../src/release/parallel_blat.cpp: In function ‘void CreateFile(const string&)’: ../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 47 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function ‘void RemoveFile(const string&)’: ../src/release/parallel_blat.cpp:53:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 53 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function ‘void Append(const string&, const string&)’: ../src/release/parallel_blat.cpp:59:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 59 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ ../src/release/parallel_blat.cpp: In function ‘void RunBlat(const string&)’: ../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] 96 | system(cmd.c_str()); | ~~~~~~^~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp ../src/release/sim_reads_tran.cpp: In function ‘int main(int, char**)’: ../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] 89 | fscanf(flist, "%s %lf", buf, &weight[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic s390x-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp s390x-linux-gnu-g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic make[3]: Leaving directory '/<>/bin' Making all in test make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/test' Making all in script make[3]: Entering directory '/<>/script' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/script' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' Making install in lib make[2]: Entering directory '/<>/lib' make[3]: Entering directory '/<>/lib' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/lib' make[2]: Leaving directory '/<>/lib' Making install in bin make[2]: Entering directory '/<>/bin' make[3]: Entering directory '/<>/bin' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/<>/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/bin' make[2]: Leaving directory '/<>/bin' Making install in test make[2]: Entering directory '/<>/test' make[3]: Entering directory '/<>/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>/test' Making install in script make[2]: Entering directory '/<>/script' make[3]: Entering directory '/<>/script' /bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/<>/debian/tmp/usr/bin' make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>/script' make[2]: Leaving directory '/<>/script' make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # for the moment the role of these scripts is totally unknown but they do not seem to be necessary mv debian/idba/usr/bin/*.py debian/idba/usr/lib/idba/ mv debian/idba/usr/bin/validate_blat* debian/idba/usr/lib/idba/ make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_missing: warning: usr/bin/run-unittest.py exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: idba (7), idba-extra (23) * dh_installdocs: idba (0), idba-extra (0) * dh_installexamples: idba (5), idba-extra (0) * dh_installman: idba (4), idba-extra (5) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built For a short-term work-around: Add the files to debian/not-installed dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'idba' in '../idba_1.1.3-7_s390x.deb'. dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-7_s390x.deb'. dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-7_s390x.deb'. dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-7_s390x.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../idba_1.1.3-7_s390x.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 2020-06-02T11:51:11Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ idba_1.1.3-7_s390x.changes: --------------------------- Format: 1.8 Date: Sat, 18 Apr 2020 08:20:19 +0200 Source: idba Binary: idba idba-dbgsym idba-extra idba-extra-dbgsym Built-For-Profiles: cross nocheck Architecture: s390x Version: 1.1.3-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: idba - iterative De Bruijn Graph short read assemblers idba-extra - iterative De Bruijn Graph short read assemblers (extra tools) Changes: idba (1.1.3-7) unstable; urgency=medium . * Rules-Requires-Root: no (routine-update) Checksums-Sha1: 0b4753999d3e5a4d44bbf77b4707268850401296 11114056 idba-dbgsym_1.1.3-7_s390x.deb 16ecdf1813b7c777fb0f46978f5760fef44e3b74 8769412 idba-extra-dbgsym_1.1.3-7_s390x.deb ed1072e6b3f386af7bec16791de3a559dabc8733 368476 idba-extra_1.1.3-7_s390x.deb d734df2dd18a99133fc068a45aa2bb1fd3e06b51 5013 idba_1.1.3-7_s390x.buildinfo b760c6afa4d32007e029859dfef426e0b0936127 625144 idba_1.1.3-7_s390x.deb Checksums-Sha256: 72dd29d1fee1651bc0cfab0b4cb70cd4087bbb1732e54f225640754705f56727 11114056 idba-dbgsym_1.1.3-7_s390x.deb 92cef74b5ce94deccdbdee862a174f9e97b80c91b219572735e123790d712020 8769412 idba-extra-dbgsym_1.1.3-7_s390x.deb e01e97e6421bc835f58e395613c7e8d8dcb75b0e3ba2b44646a2047a3832c89a 368476 idba-extra_1.1.3-7_s390x.deb 44053b2d3685501b3e3f70120ef25d707b50163d4b6724636364802a5fb0ddd5 5013 idba_1.1.3-7_s390x.buildinfo d3d286a11e554fc3a6ffb93970893a7062759c7566c011cc04870b3f130ec968 625144 idba_1.1.3-7_s390x.deb Files: e31aa2d4f5a1a172559edcb112f5331b 11114056 debug optional idba-dbgsym_1.1.3-7_s390x.deb 7d0358a2777a0e7c40049e9215f8032d 8769412 debug optional idba-extra-dbgsym_1.1.3-7_s390x.deb b8fcbb326cf11955afb77233f193aa0f 368476 science optional idba-extra_1.1.3-7_s390x.deb 1c240a7be2f48c6bd31e7215c9d391c3 5013 science optional idba_1.1.3-7_s390x.buildinfo a9bf6b5ab705401f9362ef8db6e54350 625144 science optional idba_1.1.3-7_s390x.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: idba Binary: idba idba-extra Architecture: s390x Version: 1.1.3-7 Checksums-Md5: e31aa2d4f5a1a172559edcb112f5331b 11114056 idba-dbgsym_1.1.3-7_s390x.deb 7d0358a2777a0e7c40049e9215f8032d 8769412 idba-extra-dbgsym_1.1.3-7_s390x.deb b8fcbb326cf11955afb77233f193aa0f 368476 idba-extra_1.1.3-7_s390x.deb a9bf6b5ab705401f9362ef8db6e54350 625144 idba_1.1.3-7_s390x.deb Checksums-Sha1: 0b4753999d3e5a4d44bbf77b4707268850401296 11114056 idba-dbgsym_1.1.3-7_s390x.deb 16ecdf1813b7c777fb0f46978f5760fef44e3b74 8769412 idba-extra-dbgsym_1.1.3-7_s390x.deb ed1072e6b3f386af7bec16791de3a559dabc8733 368476 idba-extra_1.1.3-7_s390x.deb b760c6afa4d32007e029859dfef426e0b0936127 625144 idba_1.1.3-7_s390x.deb Checksums-Sha256: 72dd29d1fee1651bc0cfab0b4cb70cd4087bbb1732e54f225640754705f56727 11114056 idba-dbgsym_1.1.3-7_s390x.deb 92cef74b5ce94deccdbdee862a174f9e97b80c91b219572735e123790d712020 8769412 idba-extra-dbgsym_1.1.3-7_s390x.deb e01e97e6421bc835f58e395613c7e8d8dcb75b0e3ba2b44646a2047a3832c89a 368476 idba-extra_1.1.3-7_s390x.deb d3d286a11e554fc3a6ffb93970893a7062759c7566c011cc04870b3f130ec968 625144 idba_1.1.3-7_s390x.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 02 Jun 2020 11:51:11 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-1), 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), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.35.2-2), build-essential (= 12.8), bzip2 (= 1.0.8-3), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-9 (= 9.3.0-13), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.1), debianutils (= 4.11), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.8.1-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.3.0-13), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10.1.0-3), gcc-9 (= 9.3.0-13), gcc-9-base (= 9.3.0-13), 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 (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan5 (= 9.3.0-13), libatomic1 (= 10.1.0-3), 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 (= 2.35.2-2), libbsd0 (= 0.10.0-1), 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 (= 0.7.9-2.1+b2), libcc1-0 (= 10.1.0-3), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1), libcrypt1 (= 1:4.4.16-1), libctf-nobfd0 (= 2.34-8), libctf0 (= 2.34-8), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.252), libdebhelper-perl (= 13.1), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.8.1-1), libgcc-9-dev (= 9.3.0-13), libgcc-s1 (= 10.1.0-3), libgcrypt20 (= 1.8.5-5), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.3-1), libgmp10 (= 2:6.2.0+dfsg-4), libgomp1 (= 10.1.0-3), libgpg-error0 (= 1.37-1), libicu63 (= 63.2-3), libisl22 (= 0.22.1-1), libitm1 (= 10.1.0-3), liblsan0 (= 10.1.0-3), liblz4-1 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./usr/share/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-04-18 06:20 ./usr/share/doc/idba-extra-dbgsym -> idba-extra idba-extra_1.1.3-7_s390x.deb ---------------------------- new Debian package, version 2.0. size 368476 bytes: control archive=1876 bytes. 1473 bytes, 30 lines control 1765 bytes, 30 lines md5sums Package: idba-extra Source: idba Version: 1.1.3-7 Architecture: s390x Maintainer: Debian Med Packaging Team Installed-Size: 2575 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 5.2), python3, idba Section: science Priority: optional Homepage: https://github.com/loneknightpy/idba Description: iterative De Bruijn Graph short read assemblers (extra tools) IDBA stands for iterative de Bruijn graph assembler. In computational sequence biology, an assembler solves the puzzle coming from large sequencing machines that feature many gigabytes of short reads from a large genome. . This package provides several flavours of the IDBA assembler, as they all share the same source tree but serve different purposes and evolved over time. . IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data. . This package ships extra tools for using idba in specific situations. drwxr-xr-x root/root 0 2020-04-18 06:20 ./ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/bin/ -rwxr-xr-x root/root 47432 2020-04-18 06:20 ./usr/bin/fa2fq -rwxr-xr-x root/root 51448 2020-04-18 06:20 ./usr/bin/filter_blat -rwxr-xr-x root/root 47440 2020-04-18 06:20 ./usr/bin/filter_contigs -rwxr-xr-x root/root 51528 2020-04-18 06:20 ./usr/bin/fq2fa -rwxr-xr-x root/root 76112 2020-04-18 06:20 ./usr/bin/parallel_blat -rwxr-xr-x root/root 76112 2020-04-18 06:20 ./usr/bin/parallel_rna_blat -rwxr-xr-x root/root 313696 2020-04-18 06:20 ./usr/bin/print_graph -rwxr-xr-x root/root 72016 2020-04-18 06:20 ./usr/bin/raw_n50 -rwxr-xr-x root/root 88424 2020-04-18 06:20 ./usr/bin/sample_reads -rwxr-xr-x root/root 644528 2020-04-18 06:20 ./usr/bin/scaffold -rwxr-xr-x root/root 76104 2020-04-18 06:20 ./usr/bin/shuffle_reads -rwxr-xr-x root/root 88424 2020-04-18 06:20 ./usr/bin/sim_reads -rwxr-xr-x root/root 88424 2020-04-18 06:20 ./usr/bin/sim_reads_tran -rwxr-xr-x root/root 67832 2020-04-18 06:20 ./usr/bin/sort_psl -rwxr-xr-x root/root 84296 2020-04-18 06:20 ./usr/bin/sort_reads -rwxr-xr-x root/root 47432 2020-04-18 06:20 ./usr/bin/split_fa -rwxr-xr-x root/root 47432 2020-04-18 06:20 ./usr/bin/split_fq -rwxr-xr-x root/root 59720 2020-04-18 06:20 ./usr/bin/split_scaffold -rwxr-xr-x root/root 125256 2020-04-18 06:20 ./usr/bin/validate_component -rwxr-xr-x root/root 108872 2020-04-18 06:20 ./usr/bin/validate_contigs_blat -rwxr-xr-x root/root 117096 2020-04-18 06:20 ./usr/bin/validate_contigs_mummer -rwxr-xr-x root/root 112968 2020-04-18 06:20 ./usr/bin/validate_reads_blat -rwxr-xr-x root/root 108872 2020-04-18 06:20 ./usr/bin/validate_rna drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba-extra/ -rw-r--r-- root/root 1735 2020-04-18 06:20 ./usr/share/doc/idba-extra/changelog.Debian.gz -rw-r--r-- root/root 2585 2020-04-18 06:20 ./usr/share/doc/idba-extra/copyright drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/man/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/man/man1/ -rw-r--r-- root/root 416 2020-04-18 06:20 ./usr/share/man/man1/filter_blat.1.gz -rw-r--r-- root/root 438 2020-04-18 06:20 ./usr/share/man/man1/filter_contigs.1.gz -rw-r--r-- root/root 426 2020-04-18 06:20 ./usr/share/man/man1/fq2fa.1.gz -rw-r--r-- root/root 483 2020-04-18 06:20 ./usr/share/man/man1/sim_reads.1.gz -rw-r--r-- root/root 460 2020-04-18 06:20 ./usr/share/man/man1/sim_reads_tran.1.gz idba_1.1.3-7_s390x.deb ---------------------- new Debian package, version 2.0. size 625144 bytes: control archive=1696 bytes. 1360 bytes, 27 lines control 1599 bytes, 23 lines md5sums Package: idba Version: 1.1.3-7 Architecture: s390x Maintainer: Debian Med Packaging Team Installed-Size: 4358 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libstdc++6 (>= 5.2), python3 Section: science Priority: optional Homepage: https://github.com/loneknightpy/idba Description: iterative De Bruijn Graph short read assemblers IDBA stands for iterative de Bruijn graph assembler. In computational sequence biology, an assembler solves the puzzle coming from large sequencing machines that feature many gigabytes of short reads from a large genome. . This package provides several flavours of the IDBA assembler, as they all share the same source tree but serve different purposes and evolved over time. . IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data. drwxr-xr-x root/root 0 2020-04-18 06:20 ./ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/bin/ -rwxr-xr-x root/root 685480 2020-04-18 06:20 ./usr/bin/idba -rwxr-xr-x root/root 779688 2020-04-18 06:20 ./usr/bin/idba_hybrid -rwxr-xr-x root/root 694632 2020-04-18 06:20 ./usr/bin/idba_tran -rwxr-xr-x root/root 771496 2020-04-18 06:20 ./usr/bin/idba_ud drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/lib/idba/ -rwxr-xr-x root/root 4144 2020-04-18 06:20 ./usr/lib/idba/scan.py -rwxr-xr-x root/root 301 2020-04-18 06:20 ./usr/lib/idba/validate_blat -rwxr-xr-x root/root 223 2020-04-18 06:20 ./usr/lib/idba/validate_blat_parallel drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba/ -rw-r--r-- root/root 1735 2020-04-18 06:20 ./usr/share/doc/idba/changelog.Debian.gz -rw-r--r-- root/root 2585 2020-04-18 06:20 ./usr/share/doc/idba/copyright drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba/examples/ -rw-r--r-- root/root 1015 2020-04-18 06:20 ./usr/share/doc/idba/examples/README -rw-r--r-- root/root 719 2020-04-18 06:20 ./usr/share/doc/idba/examples/data-source.sh drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba/examples/hybrid/ -rw-r--r-- root/root 10750 2020-04-18 06:20 ./usr/share/doc/idba/examples/hybrid/ecoli_ref.fa -rw-r--r-- root/root 5085 2020-04-18 06:20 ./usr/share/doc/idba/examples/hybrid/ecoli_target.fa -rw-r--r-- root/root 10732 2020-04-18 06:20 ./usr/share/doc/idba/examples/hybrid/efergusonii_ref.fa drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba/examples/tran/ -rw-r--r-- root/root 565135 2020-04-18 06:20 ./usr/share/doc/idba/examples/tran/found-transcripts.fa -rw-r--r-- root/root 886740 2020-04-18 06:20 ./usr/share/doc/idba/examples/tran/found-transcripts.fa.list drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/doc/idba/examples/ud/ -rw-r--r-- root/root 5072 2020-04-18 06:20 ./usr/share/doc/idba/examples/ud/220668.fa -rw-r--r-- root/root 5098 2020-04-18 06:20 ./usr/share/doc/idba/examples/ud/321956.fa -rw-r--r-- root/root 5084 2020-04-18 06:20 ./usr/share/doc/idba/examples/ud/557433.fa drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/man/ drwxr-xr-x root/root 0 2020-04-18 06:20 ./usr/share/man/man1/ -rw-r--r-- root/root 813 2020-04-18 06:20 ./usr/share/man/man1/idba.1.gz -rw-r--r-- root/root 941 2020-04-18 06:20 ./usr/share/man/man1/idba_hybrid.1.gz -rw-r--r-- root/root 856 2020-04-18 06:20 ./usr/share/man/man1/idba_tran.1.gz -rw-r--r-- root/root 905 2020-04-18 06:20 ./usr/share/man/man1/idba_ud.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 [558 B] Get:5 copy:/<>/apt_archive ./ Packages [620 B] Fetched 2141 B in 0s (82.2 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... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: libclass-xsaccessor-perl : Depends: perl (< 5.30.3~) but 5.30.3-1 is to be installed E: Unable to correct problems, you have held broken packages. apt-get failed. E: Package installation failed Not removing build depends: cloned chroot in use +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 396824 Build-Time: 218 Distribution: unstable Foreign Architectures: s390x Host Architecture: s390x Install-Time: 18 Job: idba_1.1.3-7 Lintian: error Machine Architecture: amd64 Package: idba Package-Time: 246 Source-Version: 1.1.3-7 Space: 396824 Status: successful Version: 1.1.3-7 -------------------------------------------------------------------------------- Finished at 2020-06-02T11:51:11Z Build needed 00:04:06, 396824k disk space