sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Thu, 15 May 2025 03:39:50 +0000 | +==============================================================================+ Package: proteinortho Version: 6.3.1+dfsg-1 Source Version: 6.3.1+dfsg-1 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild._H7MjAKnYs... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-o8bAeX/resolver-A6hciF' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [205 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.0 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.0 MB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [10.1 MB] Fetched 31.3 MB in 7s (4363 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 73.1 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 base-files arm64 13.8 [73.1 kB] Fetched 73.1 kB in 0s (2487 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 ... 12033 files and directories currently installed.) Preparing to unpack .../base-files_13.8_arm64.deb ... Unpacking base-files (13.8) over (13.7) ... Setting up base-files (13.8) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://mirror.einval.org/debian unstable/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://mirror.einval.org/debian unstable/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (5517 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/proteinortho-o8bAeX/proteinortho-6.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-o8bAeX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner (>= 2.0.10~), procps, debhelper, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 998:999 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [826 B] Get:5 copy:/<>/apt_archive ./ Packages [834 B] Fetched 2269 B in 0s (89.4 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... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner:amd64 dwz fakeroot file g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-14-base:amd64 gcc-14-cross-base gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:amd64 libgcc-14-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblmdb0 liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 libstdc++-14-dev:amd64 libstdc++-14-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libuv1t64 libxml2 linux-libc-dev-amd64-cross m4 man-db media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sensible-utils tzdata zlib1g:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales cpp-14-doc cpp-doc dh-make gcc-14-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libstdc++-14-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support readline-doc Recommended packages: med-config:amd64 curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner:amd64 dwz fakeroot file g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-14-base:amd64 gcc-14-cross-base gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:amd64 libgcc-14-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblmdb0 liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 libstdc++-14-dev:amd64 libstdc++-14-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libuv1t64 libxml2 linux-libc-dev-amd64-cross m4 man-db media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils tzdata zlib1g:amd64 0 upgraded, 110 newly installed, 0 to remove and 0 not upgraded. Need to get 134 MB of archives. After this operation, 586 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2025b-3 [260 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.5+20250216-2 [124 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-8 [1131 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 gcc-14-x86-64-linux-gnu-base arm64 14.2.0-19cross1 [49.6 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 cpp-14-x86-64-linux-gnu arm64 14.2.0-19cross1 [10.4 MB] Get:36 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:14.2.0-1 [4852 B] Get:37 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.44-3 [1483 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14.2.0-19cross1 [44.9 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 14.2.0-19cross1 [72.8 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 14.2.0-19cross1 [129 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 14.2.0-19cross1 [25.4 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 14.2.0-19cross1 [8972 B] Get:43 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 14.2.0-19cross1 [2713 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 14.2.0-19cross1 [1203 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 14.2.0-19cross1 [2448 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.41-6cross2 [1558 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 14.2.0-19cross1 [665 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 14.2.0-19cross1 [1073 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 14.2.0-19cross1 [1484 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 14.2.0-19cross1 [145 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libgcc-14-dev-amd64-cross all 14.2.0-19cross1 [2665 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 gcc-14-x86-64-linux-gnu arm64 14.2.0-19cross1 [20.0 MB] Get:53 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:14.2.0-1 [1448 B] Get:54 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.12.17-1cross2 [2369 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.41-6cross2 [1987 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libstdc++-14-dev-amd64-cross all 14.2.0-19cross1 [2354 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 g++-14-x86-64-linux-gnu arm64 14.2.0-19cross1 [11.2 MB] Get:58 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:14.2.0-1 [1204 B] Get:59 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:60 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:66 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.41-7 [2847 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.37.1.2-1 [29.7 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.37.1.2-1 [75.4 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 14.2.0-19 [2725 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:84 http://mirror.einval.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.41-7 [1992 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 liblmdb0 arm64 0.9.31-1+b2 [43.5 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libmbedcrypto16 arm64 3.6.3-1 [343 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libmbedx509-7 arm64 3.6.3-1 [148 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libmbedtls21 arm64 3.6.3-1 [224 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get:107 http://mirror.einval.org/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 ncbi-blast+ arm64 2.16.0+ds-7 [14.5 MB] Preconfiguring packages ... 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Setting up libfakeroot:arm64 (1.37.1.2-1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu May 15 03:41:18 UTC 2025. Universal Time is now: Thu May 15 03:41:18 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.37.1.2-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libitm1-amd64-cross (14.2.0-19cross1) ... Setting up autotools-dev (20240727.1) ... Setting up libatomic1-amd64-cross (14.2.0-19cross1) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libquadmath0-amd64-cross (14.2.0-19cross1) ... Setting up autopoint (0.23.1-2) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-19cross1) ... Setting up libc6-amd64-cross (2.41-6cross2) ... Setting up libncursesw6:arm64 (6.5+20250216-2) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:arm64 (3.6.3-1) ... Setting up libgcc-s1-amd64-cross (14.2.0-19cross1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up binutils-x86-64-linux-gnu (2.44-3) ... Setting up libstdc++6-amd64-cross (14.2.0-19cross1) ... Setting up cpp-x86-64-linux-gnu (4:14.2.0-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libasan8-amd64-cross (14.2.0-19cross1) ... Setting up liblsan0-amd64-cross (14.2.0-19cross1) ... Setting up libc6-dev-amd64-cross (2.41-6cross2) ... Setting up libtsan2-amd64-cross (14.2.0-19cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:arm64 (3.6.3-1) ... Setting up libhwasan0-amd64-cross (14.2.0-19cross1) ... Setting up libubsan1-amd64-cross (14.2.0-19cross1) ... Setting up libmbedtls21:arm64 (3.6.3-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libgcc-14-dev-amd64-cross (14.2.0-19cross1) ... Setting up groff-base (1.23.0-8) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-19cross1) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libstdc++-14-dev-amd64-cross (14.2.0-19cross1) ... Setting up gcc-x86-64-linux-gnu (4:14.2.0-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.3-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up g++-14-x86-64-linux-gnu (14.2.0-19cross1) ... Setting up g++-x86-64-linux-gnu (4:14.2.0-1) ... Setting up debhelper (13.24.2) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (14.2.0-19) ... Setting up libc6:amd64 (2.41-7) ... Setting up libhwasan0:amd64 (14.2.0-19) ... Setting up libasan8:amd64 (14.2.0-19) ... Setting up libtsan2:amd64 (14.2.0-19) ... Setting up libstdc++6:amd64 (14.2.0-19) ... Setting up liblsan0:amd64 (14.2.0-19) ... Setting up libitm1:amd64 (14.2.0-19) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libcrypt1:amd64 (1:4.4.38-1) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up diamond-aligner:amd64 (2.1.11-2) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libquadmath0:amd64 (14.2.0-19) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libubsan1:amd64 (14.2.0-19) ... Setting up libcrypt-dev:amd64 (1:4.4.38-1) ... Setting up libc6-dev:amd64 (2.41-7) ... Setting up libgcc-14-dev:amd64 (14.2.0-19) ... Setting up libstdc++-14-dev:amd64 (14.2.0-19) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up liblapack-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (13.8) ... Processing triggers for libc-bin (2.41-7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) arm64 (aarch64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-7 libstdc++-14-dev_14.2.0-19 libstdc++-14-dev-amd64-cross_14.2.0-19cross1 libstdc++6_14.2.0-19 libstdc++6-amd64-cross_14.2.0-19cross1 linux-libc-dev_6.12.27-1 Package versions: apt_3.0.1 apt-utils_3.0.1 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b1 binutils_2.44-3 binutils-aarch64-linux-gnu_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-2 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-aarch64-linux-gnu_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19cross1 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-amd64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.22 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diamond-aligner_2.1.11-2 diffutils_1:3.10-4 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 fakeroot_1.37.1.2-1 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-19 g++-14-aarch64-linux-gnu_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19cross1 g++-aarch64-linux-gnu_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-19 gcc-14-aarch64-linux-gnu_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-cross-base_14.2.0-19cross1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.3.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper Package-List: proteinortho deb science optional arch=any Checksums-Sha1: 36ddff1bcbf8dde0a19795f74e154e74aadc1705 375988 proteinortho_6.3.1+dfsg.orig.tar.xz d2526cacd7835c2f294f0219e9514a1644f13e78 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Checksums-Sha256: 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PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc make[1]: Entering directory '/<>' CC = x86_64-linux-gnu-gcc CCFLAGS = CXX = x86_64-linux-gnu-g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = FALSE Creating build directory ... [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) x86_64-linux-gnu-g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_aarch64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive /bin/sh: 1: src/BUILD/Linux_aarch64/proteinortho_clustering: Exec format error ......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX). x86_64-linux-gnu-g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_aarch64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -lpthread /bin/sh: 3: src/BUILD/Linux_aarch64/proteinortho_clustering: Exec format error ......dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas. x86_64-linux-gnu-g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_aarch64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -lopenblas -pthread -lpthread /usr/lib/gcc-cross/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/bin/ld: cannot find -lopenblas: No such file or directory collect2: error: ld returned 1 exit status ......last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking. ......[ 33%] Extracting the LAPACK library cd src; tar -xzvf lapack-3.8.0.tar.gz ......[ 66%] Compiling the LAPACK library (using cmake + make) mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=x86_64-linux-gnu-g++ > /dev/null; make all -j4 /bin/sh: 10: cd: can't cd to src/lapack-3.8.0/build /bin/sh: 10: cmake: not found E: Build killed with signal TERM after 150 minutes of inactivity -------------------------------------------------------------------------------- Build finished at 2025-05-15T06:16:49Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands | +------------------------------------------------------------------------------+ rm -Rf /<>/ ---------------------------------------------------------- I: Finished running 'rm -Rf /<>/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 9321 Distribution: unstable Fail-Stage: build Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 61 Job: proteinortho_6.3.1+dfsg-1 Machine Architecture: arm64 Package: proteinortho Package-Time: 9419 Source-Version: 6.3.1+dfsg-1 Space: n/a Status: attempted Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-05-15T06:16:49Z Build needed 02:36:59, no disk space