sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (arm64) Wed, 09 Jul 2025 20:18:02 +0000 | +==============================================================================+ Package: proteinortho Version: 6.3.1+dfsg-1 Source Version: 6.3.1+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-9043fedb-1c91-4608-86cd-17b757afa167' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-guhIPL/resolver-hAZXbG' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [213 kB] Get:2 http://localhost:3142/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian unstable/main Sources T-2025-07-09-1404.44-F-2025-07-09-0253.04.pdiff [16.8 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2025-07-09-1404.44-F-2025-07-09-0253.04.pdiff [15.5 kB] Get:4 http://localhost:3142/debian unstable/main Sources T-2025-07-09-1404.44-F-2025-07-09-0253.04.pdiff [16.8 kB] Get:6 http://localhost:3142/debian unstable/main arm64 Packages [10.0 MB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages T-2025-07-09-1404.44-F-2025-07-09-0253.04.pdiff [15.5 kB] Fetched 10.4 MB in 3s (3841 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: '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://localhost:3142/debian unstable/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://localhost:3142/debian unstable/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://localhost:3142/debian unstable/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 1s (635 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/proteinortho-guhIPL/proteinortho-6.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-guhIPL' 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:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner (>= 2.0.10~), procps, debhelper, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119 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 (0 B/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-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner:arm64 dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libblas-dev:arm64 libblas3:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64 libhwasan0-arm64-cross libitm1:arm64 libitm1-arm64-cross liblapack-dev:arm64 liblapack3:arm64 liblmdb0 liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring5 libuv1t64 libxml2 linux-libc-dev-arm64-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 zlib1g:arm64 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-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 libstdc++-14-doc:arm64 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:arm64 curl | wget | lynx libidn2-0:arm64 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-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner:arm64 dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libblas-dev:arm64 libblas3:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgomp1:arm64 libgomp1-arm64-cross libhwasan0:arm64 libhwasan0-arm64-cross libitm1:arm64 libitm1-arm64-cross liblapack-dev:arm64 liblapack3:arm64 liblmdb0 liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunistring5 libuv1t64 libxml2 linux-libc-dev-arm64-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:arm64 sensible-utils zlib1g:arm64 0 upgraded, 107 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://localhost:3142/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB] Get:4 http://localhost:3142/debian unstable/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:5 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:6 http://localhost:3142/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get:7 http://localhost:3142/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:10 http://localhost:3142/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 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amd64 0.23.1-2 [243 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:24 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:25 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:27 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:28 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:29 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:30 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:31 http://localhost:3142/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:32 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:33 http://localhost:3142/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.44-3 [1687 kB] Get:34 http://localhost:3142/debian unstable/main amd64 gcc-14-aarch64-linux-gnu-base amd64 14.2.0-19cross1 [49.7 kB] Get:35 http://localhost:3142/debian unstable/main amd64 cpp-14-aarch64-linux-gnu amd64 14.2.0-19cross1 [11.2 MB] Get:36 http://localhost:3142/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:14.2.0-1 [4844 B] Get:37 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base all 14.2.0-19cross1 [44.9 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libc6-arm64-cross all 2.41-8cross1 [1165 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libgcc-s1-arm64-cross all 14.2.0-19cross1 [54.1 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libgomp1-arm64-cross all 14.2.0-19cross1 [91.7 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libitm1-arm64-cross all 14.2.0-19cross1 [26.0 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libatomic1-arm64-cross all 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Get:52 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-arm64-cross all 6.12.29-1cross1 [2397 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libc6-dev-arm64-cross all 2.41-8cross1 [1616 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev-arm64-cross all 14.2.0-19cross1 [2552 kB] Get:55 http://localhost:3142/debian unstable/main amd64 g++-14-aarch64-linux-gnu amd64 14.2.0-19cross1 [12.2 MB] Get:56 http://localhost:3142/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:14.2.0-1 [1200 B] Get:57 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-arm64 all 12.12 [3548 B] Get:58 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:60 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:63 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:64 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:65 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:68 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:69 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:70 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:71 http://localhost:3142/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:72 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arm64 3.12.1-2 [104 kB] Get:83 http://localhost:3142/debian unstable/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get:84 http://localhost:3142/debian unstable/main arm64 libcrypt1 arm64 1:4.4.38-1 [91.8 kB] Get:85 http://localhost:3142/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.38-1 [123 kB] Get:86 http://localhost:3142/debian unstable/main arm64 libc6-dev arm64 2.41-9 [1622 kB] Get:87 http://localhost:3142/debian unstable/main arm64 libgomp1 arm64 14.2.0-19 [124 kB] Get:88 http://localhost:3142/debian unstable/main arm64 libitm1 arm64 14.2.0-19 [24.2 kB] Get:89 http://localhost:3142/debian unstable/main arm64 liblsan0 arm64 14.2.0-19 [1161 kB] Get:90 http://localhost:3142/debian unstable/main arm64 libtsan2 arm64 14.2.0-19 [2383 kB] Get:91 http://localhost:3142/debian unstable/main arm64 libubsan1 arm64 14.2.0-19 [1039 kB] Get:92 http://localhost:3142/debian unstable/main arm64 libhwasan0 arm64 14.2.0-19 [1442 kB] Get:93 http://localhost:3142/debian unstable/main arm64 libgcc-14-dev arm64 14.2.0-19 [2359 kB] Get:94 http://localhost:3142/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get:95 http://localhost:3142/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get:96 http://localhost:3142/debian unstable/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get:97 http://localhost:3142/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB] Get:101 http://localhost:3142/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:104 http://localhost:3142/debian unstable/main arm64 libstdc++-14-dev arm64 14.2.0-19 [2295 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:106 http://localhost:3142/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:107 http://localhost:3142/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Preconfiguring packages ... Fetched 126 MB in 1s (113 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... 12887 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ... Unpacking python3.13-minimal (3.13.5-2) ... Setting up libpython3.13-minimal:amd64 (3.13.5-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13221 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_amd64.deb ... Unpacking python3-minimal (3.13.5-1) ... 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Setting up liblsan0-arm64-cross (14.2.0-19cross1) ... Setting up libgomp1-arm64-cross (14.2.0-19cross1) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up libhwasan0-arm64-cross (14.2.0-19cross1) ... Setting up libc6-dev-arm64-cross (2.41-8cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (14.2.0-19cross1) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.3-1) ... Setting up libmbedtls21:amd64 (3.6.3-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up cpp-14-aarch64-linux-gnu (14.2.0-19cross1) ... Setting up groff-base (1.23.0-9) ... Setting up libasan8-arm64-cross (14.2.0-19cross1) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libtsan2-arm64-cross (14.2.0-19cross1) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libubsan1-arm64-cross (14.2.0-19cross1) ... Setting up python3.13 (3.13.5-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up python3 (3.13.5-1) ... 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 cpp-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libgcc-14-dev-arm64-cross (14.2.0-19cross1) ... Setting up libstdc++-14-dev-arm64-cross (14.2.0-19cross1) ... Setting up gcc-14-aarch64-linux-gnu (14.2.0-19cross1) ... Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ... Setting up g++-14-aarch64-linux-gnu (14.2.0-19cross1) ... Setting up debhelper (13.24.2) ... Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ... Setting up crossbuild-essential-arm64 (12.12) ... Setting up libgcc-s1:arm64 (14.2.0-19) ... Setting up libc6:arm64 (2.41-9) ... Setting up libhwasan0:arm64 (14.2.0-19) ... Setting up libasan8:arm64 (14.2.0-19) ... Setting up libtsan2:arm64 (14.2.0-19) ... Setting up libstdc++6:arm64 (14.2.0-19) ... Setting up liblsan0:arm64 (14.2.0-19) ... Setting up libitm1:arm64 (14.2.0-19) ... Setting up zlib1g:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libcrypt1:arm64 (1:4.4.38-1) ... Setting up libgomp1:arm64 (14.2.0-19) ... Setting up diamond-aligner:arm64 (2.1.11-2) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libatomic1:arm64 (14.2.0-19) ... Setting up libgfortran5:arm64 (14.2.0-19) ... Setting up libubsan1:arm64 (14.2.0-19) ... Setting up libcrypt-dev:arm64 (1:4.4.38-1) ... Setting up libc6-dev:arm64 (2.41-9) ... Setting up libgcc-14-dev:arm64 (14.2.0-19) ... Setting up libstdc++-14-dev:arm64 (14.2.0-19) ... Setting up libblas-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up liblapack-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.21 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-14-dev_14.2.0-19 libstdc++-14-dev-arm64-cross_14.2.0-19cross1 libstdc++6_14.2.0-19 libstdc++6-arm64-cross_14.2.0-19cross1 linux-libc-dev_6.12.35-1 Package versions: apt_3.0.3 apt-utils_3.0.3 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+b3 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_9.7-3 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-aarch64-linux-gnu_14.2.0-19cross1 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-arm64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diamond-aligner_2.1.11-2 diffutils_1:3.10-4 dpkg_1.22.21 dpkg-dev_1.22.21 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_14.2.0-19cross1 g++-14-x86-64-linux-gnu_14.2.0-19 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_14.2.0-19cross1 gcc-14-aarch64-linux-gnu-base_14.2.0-19cross1 gcc-14-base_14.2.0-19 gcc-14-cross-base_14.2.0-19cross1 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-aarch64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libasan8-arm64-cross_14.2.0-19cross1 libatomic1_14.2.0-19 libatomic1-arm64-cross_14.2.0-19cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.44-3 libblas-dev_3.12.1-2 libblas3_3.12.1-2 libblkid1_2.41-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc6_2.41-9 libc6-arm64-cross_2.41-8cross1 libc6-dev_2.41-9 libc6-dev-arm64-cross_2.41-8cross1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdpkg-perl_1.22.21 libelf1t64_0.192-4 libexpat1_2.7.1-1 libfakeroot_1.37.1.2-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.2.0-19 libgcc-14-dev-arm64-cross_14.2.0-19cross1 libgcc-s1_14.2.0-19 libgcc-s1-arm64-cross_14.2.0-19cross1 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-19 libgmp10_2:6.3.0+dfsg-3 libgomp1_14.2.0-19 libgomp1-arm64-cross_14.2.0-19cross1 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-19 libhwasan0-arm64-cross_14.2.0-19cross1 libisl23_0.27-1 libitm1_14.2.0-19 libitm1-arm64-cross_14.2.0-19cross1 libjansson4_2.14-2+b3 liblapack-dev_3.12.1-2 liblapack3_3.12.1-2 liblastlog2-2_2.41-5 liblmdb0_0.9.31-1+b2 liblsan0_14.2.0-19 liblsan0-arm64-cross_14.2.0-19cross1 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmbedcrypto16_3.6.3-1 libmbedtls21_3.6.3-1 libmbedx509-7_3.6.3-1 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncbi-vdb3_3.2.1+dfsg-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-5 libpipeline1_1.5.8-1 libproc2-0_2:4.0.4-8 libpython3-stdlib_3.13.5-1 libpython3.13-minimal_3.13.5-2 libpython3.13-stdlib_3.13.5-2 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssl3t64_3.5.0-2 libstdc++-14-dev_14.2.0-19 libstdc++-14-dev-arm64-cross_14.2.0-19cross1 libstdc++6_14.2.0-19 libstdc++6-arm64-cross_14.2.0-19cross1 libsystemd0_257.7-1 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libtsan2-arm64-cross_14.2.0-19cross1 libubsan1_14.2.0-19 libubsan1-arm64-cross_14.2.0-19cross1 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunistring5_1.3-2 libuuid1_2.41-5 libuv1t64_1.50.0-2 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ 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: 7ce978cf6d33a6f67a3138d7f4cafe3ed5c1dcfbdd70224f1514385df9531679 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ab190de700fdc10752e33b2e0c263f6166a2dfb8d8a119d987a7265b99df61fe 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Files: 286e6fd86b91807e92db7e8bd7a3c87c 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ee4d531727d1dc02b1af12b004ed1c99 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWg1C8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHolg/8CJZu3mudXnpM0z+TV/H6OgBg+eGm/mkU opYsSgqwFb4k6PwHTa9VA3Zq+liUKDRLBvRyz0olnOff5RhE5t+xys2LMHLj+n4g Maij/jnhq+XbAefm4Z0MFg4LsVH/rrKCn+fWlCV7H4YoKL/QEkbsIebdD4l+7jhV qe1cMgEHjmG+6XccBmpii+dLyIQGGuRGIIdmaOzmxPw8EzFQkE7uOdhWG42PtPgo YVM/JZyLXe7gtY73UM8MFOTIuJ/RVOwx/BUOjuC6P9zu0TimNhwBnNvwQW+PECu5 nJWgm1mixkpGvsQSNsu7ITUPMbbr/LE9Vu7yt/1V28SbCQxgsNwuONG1+Qyao3lt vv9nhH9YUOktpfyr2dCJinpqEQ5uv1eYeSXpyNIJzwWSPeWQW+zxuPDSa0u750br C3/8UjoMWTrVDbTc0Y9CN9coUHkghXPvLsxxpqpj4gBIWgjFM3SMNP56p1Rv5uRx QZUk5F81PteMIwgkp0z3bY0ZezA2o7eLFjGmrwLwl4l0hdWrjHyhumtJuTldFZt9 HJ6rlvfDuj+Kml2uC41CMoHV5thvnQC2MjBVQjG38IYf2AAyd6oafGFA8hHqF4qu eL69T0QQeXHICNXvCE4xyjVM8xIWfeYNCbkZULbOq7bdEzueDZEP/GzLCUkM+d2d YXWwk5h9Tsw= =8nLU -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in /<> dpkg-source: info: unpacking proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.vsQdtSK3hU/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-9043fedb-1c91-4608-86cd-17b757afa167 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -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 aarch64-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 arm64 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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc make[1]: Entering directory '/<>' CC = aarch64-linux-gnu-gcc CCFLAGS = CXX = aarch64-linux-gnu-g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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) aarch64-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 -mbranch-protection=standard -fopenmp -o src/BUILD/Linux_x86_64/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_x86_64/proteinortho_clustering: Exec format error ......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX). aarch64-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 -mbranch-protection=standard -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -lpthread /bin/sh: 3: src/BUILD/Linux_x86_64/proteinortho_clustering: Exec format error ......dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas. aarch64-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 -mbranch-protection=standard -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -lopenblas -pthread -lpthread /usr/lib/gcc-cross/aarch64-linux-gnu/14/../../../../aarch64-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=aarch64-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 2025-07-09T22:49:39Z +------------------------------------------------------------------------------+ | 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: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 9072 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 13 Job: proteinortho_6.3.1+dfsg-1 Machine Architecture: amd64 Package: proteinortho Package-Time: 9097 Source-Version: 6.3.1+dfsg-1 Space: n/a Status: attempted Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-07-09T22:49:39Z Build needed 02:31:37, no disk space