sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | lumpy-sv 0.3.1+dfsg-8 (arm64) Thu, 13 Nov 2025 17:57:11 +0000 | +==============================================================================+ Package: lumpy-sv Version: 0.3.1+dfsg-8 Source Version: 0.3.1+dfsg-8 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-206f5638-da09-4893-8e93-42867b525a7f' with '<>' I: NOTICE: Log filtering will replace 'build/lumpy-sv-Sbvyto/resolver-wRbOb5' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [176 kB] Get:2 http://localhost:3142/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian unstable/contrib Sources.diff/Index [63.3 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian unstable/main Sources T-2025-11-13-0807.12-F-2025-11-13-0204.46.pdiff [15.4 kB] Get:6 http://localhost:3142/debian unstable/contrib Sources T-2025-11-13-0204.46-F-2025-11-13-0204.46.pdiff [31 B] Get:5 http://localhost:3142/debian unstable/main Sources T-2025-11-13-0807.12-F-2025-11-13-0204.46.pdiff [15.4 kB] Get:7 http://localhost:3142/debian unstable/main amd64 Packages T-2025-11-13-0807.12-F-2025-11-13-0204.46.pdiff [10.2 kB] Get:6 http://localhost:3142/debian unstable/contrib Sources T-2025-11-13-0204.46-F-2025-11-13-0204.46.pdiff [31 B] Get:7 http://localhost:3142/debian unstable/main amd64 Packages T-2025-11-13-0807.12-F-2025-11-13-0204.46.pdiff [10.2 kB] Get:8 http://localhost:3142/debian unstable/main arm64 Packages [10.1 MB] Fetched 10.5 MB in 3s (3764 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: 'lumpy-sv' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lumpy-sv.git Please use: git clone https://salsa.debian.org/med-team/lumpy-sv.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 39.4 MB of source archives. Get:1 http://localhost:3142/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://localhost:3142/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://localhost:3142/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 0s (211 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/lumpy-sv-Sbvyto/lumpy-sv-0.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/lumpy-sv-Sbvyto' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, 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), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, 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 [837 B] Get:5 copy:/<>/apt_archive ./ Packages [880 B] Fetched 2326 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 comerr-dev:arm64 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-15-aarch64-linux-gnu gcc-15-aarch64-linux-gnu-base gcc-15-base:arm64 gcc-15-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:arm64 libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbamtools-dev:arm64 libbamtools2.5.3:arm64 libbrotli-dev:arm64 libbrotli1:arm64 libbz2-1.0:arm64 libbz2-dev:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libcrypt-dev:arm64 libcrypt1:arm64 libcurl3t64-gnutls:arm64 libcurl4-gnutls-dev:arm64 libdb5.3t64:arm64 libdebhelper-perl libdeflate-dev:arm64 libdeflate0:arm64 libelf1t64 libevent-2.1-7t64:arm64 libfakeroot libfastahack-dev:arm64 libfastahack0:arm64 libffi8:arm64 libfile-stripnondeterminism-perl libgcc-15-dev:arm64 libgcc-15-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgmp-dev:arm64 libgmp10:arm64 libgmpxx4ldbl:arm64 libgnutls-dane0t64:arm64 libgnutls-openssl27t64:arm64 libgnutls28-dev:arm64 libgnutls30t64:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libgssrpc4t64:arm64 libgzstream-dev:arm64 libgzstream0:arm64 libhogweed6t64:arm64 libhts-dev:arm64 libhts3t64:arm64 libhtscodecs2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libidn2-0:arm64 libidn2-dev:arm64 libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkadm5clnt-mit12:arm64 libkadm5srv-mit12:arm64 libkdb5-10t64:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5-dev:arm64 libkrb5support0:arm64 libldap-dev:arm64 libldap2:arm64 liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1t64 libncurses6:arm64 libnettle8t64:arm64 libnghttp2-14:arm64 libnghttp2-dev:arm64 libnghttp3-9:arm64 libnghttp3-dev:arm64 libngtcp2-16:arm64 libngtcp2-crypto-gnutls-dev:arm64 libngtcp2-crypto-gnutls8:arm64 libngtcp2-dev:arm64 libp11-kit-dev:arm64 libp11-kit0:arm64 libpipeline1 libpkgconf3 libpsl-dev:arm64 libpsl5t64:arm64 librtmp-dev:arm64 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsqlite3-0:arm64 libsqlite3-dev:arm64 libssh2-1-dev:arm64 libssh2-1t64:arm64 libssl-dev:arm64 libssl3t64:arm64 libstdc++-15-dev:arm64 libstdc++-15-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtasn1-6:arm64 libtasn1-6-dev:arm64 libtinfo6:arm64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunbound8:arm64 libunistring5 libunistring5:arm64 libxml2-16 libzstd-dev:arm64 libzstd1:arm64 linux-libc-dev-arm64-cross m4 man-db nettle-dev:arm64 pkgconf:arm64 pkgconf-bin po-debconf samtools:arm64 sensible-utils zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc doc-base:arm64 gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc:arm64 libbamtools-doc:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 libcurl4-doc:arm64 libidn-dev:arm64 gmp-doc:arm64 libgmp10-doc:arm64 libmpfr-dev:arm64 dns-root-data:arm64 gnutls-bin:arm64 gnutls-doc:arm64 krb5-user:arm64 liblzma-doc:arm64 libnghttp2-doc:arm64 p11-kit-doc:arm64 sqlite3-doc:arm64 libssl-doc:arm64 libstdc++-15-doc:arm64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl cwltool:arm64 Recommended packages: curl | wget | lynx bzip2-doc:arm64 ca-certificates:arm64 libarchive-cpio-perl krb5-locales:arm64 libldap-common:arm64 libgpm2:arm64 publicsuffix:arm64 libsasl2-modules:arm64 libtasn1-doc:arm64 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils comerr-dev:arm64 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-15-aarch64-linux-gnu gcc-15-aarch64-linux-gnu-base gcc-15-base:arm64 gcc-15-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:arm64 libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libbamtools-dev:arm64 libbamtools2.5.3:arm64 libbrotli-dev:arm64 libbrotli1:arm64 libbz2-1.0:arm64 libbz2-dev:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libcrypt-dev:arm64 libcrypt1:arm64 libcurl3t64-gnutls:arm64 libcurl4-gnutls-dev:arm64 libdb5.3t64:arm64 libdebhelper-perl libdeflate-dev:arm64 libdeflate0:arm64 libelf1t64 libevent-2.1-7t64:arm64 libfakeroot libfastahack-dev:arm64 libfastahack0:arm64 libffi8:arm64 libfile-stripnondeterminism-perl libgcc-15-dev:arm64 libgcc-15-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgmp-dev:arm64 libgmp10:arm64 libgmpxx4ldbl:arm64 libgnutls-dane0t64:arm64 libgnutls-openssl27t64:arm64 libgnutls28-dev:arm64 libgnutls30t64:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libgssrpc4t64:arm64 libgzstream-dev:arm64 libgzstream0:arm64 libhogweed6t64:arm64 libhts-dev:arm64 libhts3t64:arm64 libhtscodecs2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libidn2-0:arm64 libidn2-dev:arm64 libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkadm5clnt-mit12:arm64 libkadm5srv-mit12:arm64 libkdb5-10t64:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5-dev:arm64 libkrb5support0:arm64 libldap-dev:arm64 libldap2:arm64 liblsan0:arm64 liblsan0-arm64-cross liblzma-dev:arm64 liblzma5:arm64 libmagic-mgc libmagic1t64 libncurses6:arm64 libnettle8t64:arm64 libnghttp2-14:arm64 libnghttp2-dev:arm64 libnghttp3-9:arm64 libnghttp3-dev:arm64 libngtcp2-16:arm64 libngtcp2-crypto-gnutls-dev:arm64 libngtcp2-crypto-gnutls8:arm64 libngtcp2-dev:arm64 libp11-kit-dev:arm64 libp11-kit0:arm64 libpipeline1 libpkgconf3 libpsl-dev:arm64 libpsl5t64:arm64 librtmp-dev:arm64 librtmp1:arm64 libsasl2-2:arm64 libsasl2-modules-db:arm64 libsqlite3-0:arm64 libsqlite3-dev:arm64 libssh2-1-dev:arm64 libssh2-1t64:arm64 libssl-dev:arm64 libssl3t64:arm64 libstdc++-15-dev:arm64 libstdc++-15-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtasn1-6:arm64 libtasn1-6-dev:arm64 libtinfo6:arm64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunbound8:arm64 libunistring5 libunistring5:arm64 libxml2-16 libzstd-dev:arm64 libzstd1:arm64 linux-libc-dev-arm64-cross m4 man-db nettle-dev:arm64 pkgconf:arm64 pkgconf-bin po-debconf samtools:arm64 sbuild-build-depends-main-dummy:arm64 sensible-utils zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 159 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 516 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:13 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://localhost:3142/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:17 http://localhost:3142/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.45-8 [1733 kB] Get:18 http://localhost:3142/debian unstable/main arm64 gcc-15-base arm64 15.2.0-8 [53.6 kB] Get:19 http://localhost:3142/debian unstable/main arm64 libgcc-s1 arm64 15.2.0-8 [53.4 kB] Get:20 http://localhost:3142/debian unstable/main arm64 libc6 arm64 2.41-12 [2489 kB] Get:21 http://localhost:3142/debian unstable/main arm64 libcrypt1 arm64 1:4.5.1-1 [93.9 kB] Get:22 http://localhost:3142/debian unstable/main arm64 libcrypt-dev arm64 1:4.5.1-1 [126 kB] Get:23 http://localhost:3142/debian unstable/main arm64 libc6-dev arm64 2.41-12 [1621 kB] Get:24 http://localhost:3142/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get:25 http://localhost:3142/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get:26 http://localhost:3142/debian unstable/main amd64 gcc-15-aarch64-linux-gnu-base amd64 15.2.0-7cross1 [53.5 kB] Get:27 http://localhost:3142/debian unstable/main amd64 cpp-15-aarch64-linux-gnu amd64 15.2.0-7cross1 [12.3 MB] Get:28 http://localhost:3142/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:15.2.0-4 [5292 B] Get:29 http://localhost:3142/debian unstable/main amd64 gcc-15-cross-base all 15.2.0-7cross1 [48.9 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libc6-arm64-cross all 2.41-11cross1 [1168 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libgcc-s1-arm64-cross all 15.2.0-7cross1 [53.4 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libgomp1-arm64-cross all 15.2.0-7cross1 [93.7 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libitm1-arm64-cross all 15.2.0-7cross1 [25.9 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libatomic1-arm64-cross all 15.2.0-7cross1 [10.1 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libasan8-arm64-cross all 15.2.0-7cross1 [442 kB] Get:36 http://localhost:3142/debian unstable/main amd64 liblsan0-arm64-cross all 15.2.0-7cross1 [210 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libtsan2-arm64-cross all 15.2.0-7cross1 [426 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libstdc++6-arm64-cross all 15.2.0-7cross1 [559 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libubsan1-arm64-cross all 15.2.0-7cross1 [193 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libhwasan0-arm64-cross all 15.2.0-7cross1 [266 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libgcc-15-dev-arm64-cross all 15.2.0-7cross1 [2537 kB] Get:42 http://localhost:3142/debian unstable/main amd64 gcc-15-aarch64-linux-gnu amd64 15.2.0-7cross1 [23.7 MB] Get:43 http://localhost:3142/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:15.2.0-4 [1444 B] Get:44 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-arm64-cross all 6.12.38-1cross1 [2446 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libc6-dev-arm64-cross all 2.41-11cross1 [1617 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libstdc++-15-dev-arm64-cross all 15.2.0-7cross1 [2699 kB] Get:47 http://localhost:3142/debian unstable/main amd64 g++-15-aarch64-linux-gnu amd64 15.2.0-7cross1 [13.3 MB] Get:48 http://localhost:3142/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:15.2.0-4 [1200 B] Get:49 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-arm64 all 12.12 [3548 B] Get:50 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-7 [540 kB] Get:52 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:55 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:56 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:57 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-0.3 [640 kB] Get:60 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:61 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:62 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:63 http://localhost:3142/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.37.1.2-1 [29.7 kB] Get:65 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.37.1.2-1 [76.0 kB] Get:66 http://localhost:3142/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get:67 http://localhost:3142/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get:68 http://localhost:3142/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get:69 http://localhost:3142/debian unstable/main arm64 libzstd1 arm64 1.5.7+dfsg-2 [260 kB] Get:70 http://localhost:3142/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.1-1+b1 [85.1 kB] Get:71 http://localhost:3142/debian unstable/main arm64 libssl3t64 arm64 3.5.4-1 [2725 kB] Get:72 http://localhost:3142/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get:73 http://localhost:3142/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get:74 http://localhost:3142/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get:75 http://localhost:3142/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get:76 http://localhost:3142/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get:77 http://localhost:3142/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get:78 http://localhost:3142/debian unstable/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get:79 http://localhost:3142/debian unstable/main arm64 libasan8 arm64 15.2.0-8 [2601 kB] Get:80 http://localhost:3142/debian unstable/main arm64 libatomic1 arm64 15.2.0-8 [9832 B] Get:81 http://localhost:3142/debian unstable/main arm64 libstdc++6 arm64 15.2.0-8 [647 kB] Get:82 http://localhost:3142/debian unstable/main arm64 libbamtools2.5.3 arm64 2.5.3+dfsg-1 [138 kB] Get:83 http://localhost:3142/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get:84 http://localhost:3142/debian unstable/main arm64 libbamtools-dev arm64 2.5.3+dfsg-1 [207 kB] Get:85 http://localhost:3142/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get:86 http://localhost:3142/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get:87 http://localhost:3142/debian unstable/main arm64 libbz2-1.0 arm64 1.0.8-6 [37.8 kB] Get:88 http://localhost:3142/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get:89 http://localhost:3142/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get:90 http://localhost:3142/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get:91 http://localhost:3142/debian unstable/main arm64 libgmp10 arm64 2:6.3.0+dfsg-5 [535 kB] Get:92 http://localhost:3142/debian unstable/main arm64 libnettle8t64 arm64 3.10.2-1 [305 kB] Get:93 http://localhost:3142/debian unstable/main arm64 libhogweed6t64 arm64 3.10.2-1 [332 kB] Get:94 http://localhost:3142/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get:95 http://localhost:3142/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get:96 http://localhost:3142/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get:97 http://localhost:3142/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get:98 http://localhost:3142/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get:99 http://localhost:3142/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get:100 http://localhost:3142/debian unstable/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-10 [626 kB] Get:101 http://localhost:3142/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get:102 http://localhost:3142/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get:103 http://localhost:3142/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get:104 http://localhost:3142/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get:105 http://localhost:3142/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get:106 http://localhost:3142/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get:107 http://localhost:3142/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get:108 http://localhost:3142/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get:109 http://localhost:3142/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.17.0-2 [363 kB] Get:110 http://localhost:3142/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get:111 http://localhost:3142/debian unstable/main arm64 libunbound8 arm64 1.24.1-2 [560 kB] Get:112 http://localhost:3142/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.10-3 [456 kB] Get:113 http://localhost:3142/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.10-3 [455 kB] Get:114 http://localhost:3142/debian unstable/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get:115 http://localhost:3142/debian unstable/main arm64 libp11-kit-dev arm64 0.25.9-2 [220 kB] Get:116 http://localhost:3142/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get:117 http://localhost:3142/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get:118 http://localhost:3142/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get:119 http://localhost:3142/debian unstable/main arm64 nettle-dev arm64 3.10.2-1 [1319 kB] Get:120 http://localhost:3142/debian unstable/main arm64 libgnutls28-dev arm64 3.8.10-3 [1414 kB] Get:121 http://localhost:3142/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get:122 http://localhost:3142/debian unstable/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:124 http://localhost:3142/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:125 http://localhost:3142/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get:126 http://localhost:3142/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get:127 http://localhost:3142/debian unstable/main arm64 libnghttp3-dev arm64 1.12.0-1 [91.6 kB] Get:128 http://localhost:3142/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.16.0-1 [24.6 kB] Get:129 http://localhost:3142/debian unstable/main arm64 libngtcp2-dev arm64 1.16.0-1 [183 kB] Get:130 http://localhost:3142/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get:131 http://localhost:3142/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get:132 http://localhost:3142/debian unstable/main arm64 libssl-dev arm64 3.5.4-1 [3377 kB] Get:133 http://localhost:3142/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get:134 http://localhost:3142/debian unstable/main arm64 libzstd-dev arm64 1.5.7+dfsg-2 [330 kB] Get:135 http://localhost:3142/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.17.0-2 [499 kB] Get:136 http://localhost:3142/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get:137 http://localhost:3142/debian unstable/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get:138 http://localhost:3142/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get:139 http://localhost:3142/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get:140 http://localhost:3142/debian unstable/main arm64 libgomp1 arm64 15.2.0-8 [126 kB] Get:141 http://localhost:3142/debian unstable/main arm64 libitm1 arm64 15.2.0-8 [24.0 kB] Get:142 http://localhost:3142/debian unstable/main arm64 liblsan0 arm64 15.2.0-8 [1194 kB] Get:143 http://localhost:3142/debian unstable/main arm64 libtsan2 arm64 15.2.0-8 [2399 kB] Get:144 http://localhost:3142/debian unstable/main arm64 libubsan1 arm64 15.2.0-8 [1064 kB] Get:145 http://localhost:3142/debian unstable/main arm64 libhwasan0 arm64 15.2.0-8 [1479 kB] Get:146 http://localhost:3142/debian unstable/main arm64 libgcc-15-dev arm64 15.2.0-8 [2373 kB] Get:147 http://localhost:3142/debian unstable/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-3 [7128 B] Get:148 http://localhost:3142/debian unstable/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-3 [7452 B] Get:149 http://localhost:3142/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get:150 http://localhost:3142/debian unstable/main arm64 liblzma5 arm64 5.8.1-2 [302 kB] Get:151 http://localhost:3142/debian unstable/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get:152 http://localhost:3142/debian unstable/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get:153 http://localhost:3142/debian unstable/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get:154 http://localhost:3142/debian unstable/main arm64 libtinfo6 arm64 6.5+20250216-2 [341 kB] Get:155 http://localhost:3142/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get:156 http://localhost:3142/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-8 [884 kB] Get:157 http://localhost:3142/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get:158 http://localhost:3142/debian unstable/main arm64 libstdc++-15-dev arm64 15.2.0-8 [2347 kB] Get:159 http://localhost:3142/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] Preconfiguring packages ... Fetched 123 MB in 1s (187 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 12910 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../002-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Selecting previously unselected package gcc-15-aarch64-linux-gnu-base:amd64. Preparing to unpack .../024-gcc-15-aarch64-linux-gnu-base_15.2.0-7cross1_amd64.deb ... Unpacking gcc-15-aarch64-linux-gnu-base:amd64 (15.2.0-7cross1) ... Selecting previously unselected package cpp-15-aarch64-linux-gnu. Preparing to unpack .../025-cpp-15-aarch64-linux-gnu_15.2.0-7cross1_amd64.deb ... Unpacking cpp-15-aarch64-linux-gnu (15.2.0-7cross1) ... Selecting previously unselected package cpp-aarch64-linux-gnu. Preparing to unpack .../026-cpp-aarch64-linux-gnu_4%3a15.2.0-4_amd64.deb ... Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4) ... Selecting previously unselected package gcc-15-cross-base. Preparing to unpack .../027-gcc-15-cross-base_15.2.0-7cross1_all.deb ... Unpacking gcc-15-cross-base (15.2.0-7cross1) ... Selecting previously unselected package libc6-arm64-cross. Preparing to unpack .../028-libc6-arm64-cross_2.41-11cross1_all.deb ... Unpacking libc6-arm64-cross (2.41-11cross1) ... 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Selecting previously unselected package liblsan0-arm64-cross. Preparing to unpack .../034-liblsan0-arm64-cross_15.2.0-7cross1_all.deb ... Unpacking liblsan0-arm64-cross (15.2.0-7cross1) ... Selecting previously unselected package libtsan2-arm64-cross. Preparing to unpack .../035-libtsan2-arm64-cross_15.2.0-7cross1_all.deb ... Unpacking libtsan2-arm64-cross (15.2.0-7cross1) ... Selecting previously unselected package libstdc++6-arm64-cross. Preparing to unpack .../036-libstdc++6-arm64-cross_15.2.0-7cross1_all.deb ... Unpacking libstdc++6-arm64-cross (15.2.0-7cross1) ... Selecting previously unselected package libubsan1-arm64-cross. Preparing to unpack .../037-libubsan1-arm64-cross_15.2.0-7cross1_all.deb ... Unpacking libubsan1-arm64-cross (15.2.0-7cross1) ... Selecting previously unselected package libhwasan0-arm64-cross. Preparing to unpack .../038-libhwasan0-arm64-cross_15.2.0-7cross1_all.deb ... Unpacking libhwasan0-arm64-cross (15.2.0-7cross1) ... 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Unpacking libelf1t64:amd64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../055-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../056-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../057-libxml2-16_2.15.1+dfsg-0.3_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../058-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../059-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../060-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... 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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 autotools-dev (20240727.1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libc6-arm64-cross (2.41-11cross1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up linux-libc-dev-arm64-cross (6.12.38-1cross1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up gcc-15-cross-base (15.2.0-7cross1) ... Setting up gcc-15-base:arm64 (15.2.0-8) ... Setting up libgcc-s1-arm64-cross (15.2.0-7cross1) ... Setting up libatomic1-arm64-cross (15.2.0-7cross1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblsan0-arm64-cross (15.2.0-7cross1) ... Setting up cpp-15-aarch64-linux-gnu (15.2.0-7cross1) ... Setting up libgomp1-arm64-cross (15.2.0-7cross1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up libhwasan0-arm64-cross (15.2.0-7cross1) ... Setting up libc6-dev-arm64-cross (2.41-11cross1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (15.2.0-7cross1) ... Setting up dh-autoreconf (21) ... Setting up cpp-aarch64-linux-gnu (4:15.2.0-4) ... Setting up libitm1-arm64-cross (15.2.0-7cross1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libasan8-arm64-cross (15.2.0-7cross1) ... Setting up libtsan2-arm64-cross (15.2.0-7cross1) ... Setting up libubsan1-arm64-cross (15.2.0-7cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-15-dev-arm64-cross (15.2.0-7cross1) ... Setting up libstdc++-15-dev-arm64-cross (15.2.0-7cross1) ... Setting up gcc-15-aarch64-linux-gnu (15.2.0-7cross1) ... Setting up debhelper (13.28) ... Setting up g++-15-aarch64-linux-gnu (15.2.0-7cross1) ... Setting up gcc-aarch64-linux-gnu (4:15.2.0-4) ... Setting up g++-aarch64-linux-gnu (4:15.2.0-4) ... Setting up crossbuild-essential-arm64 (12.12) ... Setting up libgcc-s1:arm64 (15.2.0-8) ... Setting up libc6:arm64 (2.41-12) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... Setting up libnghttp3-dev:arm64 (1.12.0-1) ... Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-10) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up libhwasan0:arm64 (15.2.0-8) ... Setting up libasan8:arm64 (15.2.0-8) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up libtsan2:arm64 (15.2.0-8) ... Setting up libbz2-1.0:arm64 (1.0.8-6) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libstdc++6:arm64 (15.2.0-8) ... Setting up liblsan0:arm64 (15.2.0-8) ... Setting up libitm1:arm64 (15.2.0-8) ... Setting up libtinfo6:arm64 (6.5+20250216-2) ... Setting up libhtscodecs2:arm64 (1.6.1-2) ... Setting up libzstd1:arm64 (1.5.7+dfsg-2) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libzstd-dev:arm64 (1.5.7+dfsg-2) ... Setting up liblzma5:arm64 (5.8.1-2) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libsqlite3-0:arm64 (3.46.1-8) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libdeflate0:arm64 (1.23-2) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up zlib1g:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libcrypt1:arm64 (1:4.5.1-1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up libngtcp2-dev:arm64 (1.16.0-1) ... Setting up libgomp1:arm64 (15.2.0-8) ... Setting up libfastahack0:arm64 (1.0.0+dfsg-11+b2) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up libfastahack-dev:arm64 (1.0.0+dfsg-11+b2) ... Setting up libnettle8t64:arm64 (3.10.2-1) ... Setting up libgmp10:arm64 (2:6.3.0+dfsg-5) ... Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libatomic1:arm64 (15.2.0-8) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libgzstream0:arm64 (1.5+git20171107.9a20658-3) ... Setting up liblzma-dev:arm64 (5.8.1-2) ... Setting up libubsan1:arm64 (15.2.0-8) ... Setting up libbamtools2.5.3:arm64 (2.5.3+dfsg-1) ... Setting up libhogweed6t64:arm64 (3.10.2-1) ... Setting up libcrypt-dev:arm64 (1:4.5.1-1) ... Setting up libc6-dev:arm64 (2.41-12) ... Setting up libdeflate-dev:arm64 (1.23-2) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libp11-kit-dev:arm64 (0.25.9-2) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up libnghttp2-dev:arm64 (1.64.0-1.1+b1) ... Setting up libgcc-15-dev:arm64 (15.2.0-8) ... Setting up libssl3t64:arm64 (3.5.4-1) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up libgzstream-dev:arm64 (1.5+git20171107.9a20658-3) ... Setting up libunbound8:arm64 (1.24.1-2) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Setting up libstdc++-15-dev:arm64 (15.2.0-8) ... Setting up libsqlite3-dev:arm64 (3.46.1-8) ... Setting up comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Setting up libssl-dev:arm64 (3.5.4-1) ... Setting up libidn2-dev:arm64 (2.3.8-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... Setting up libgnutls-openssl27t64:arm64 (3.8.10-3) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:arm64 (3.10.2-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.10-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libldap-dev:arm64 (2.6.10+dfsg-1) ... Setting up libbamtools-dev:arm64 (2.5.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up libgnutls28-dev:arm64 (3.8.10-3) ... Setting up libcurl3t64-gnutls:arm64 (8.17.0-2) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.16.0-1) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up samtools:arm64 (1.22.1-1) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:arm64 (8.17.0-2) ... Setting up libhts-dev:arm64 (1.22.1+ds2-1) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | 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_2.45-8 dpkg-dev_1.22.21 g++-15_15.2.0-8 gcc-15_15.2.0-8 libc6-dev_2.41-12 libstdc++-15-dev_15.2.0-8 libstdc++-15-dev-arm64-cross_15.2.0-7cross1 libstdc++6_15.2.0-8 libstdc++6-arm64-cross_15.2.0-7cross1 linux-libc-dev_6.17.7-2 Package versions: apt_3.1.12 apt-utils_3.1.12 autoconf_2.72-3.1 automake_1:1.18.1-2 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45-8 binutils-aarch64-linux-gnu_2.45-8 binutils-common_2.45-8 binutils-x86-64-linux-gnu_2.45-8 bsdextrautils_2.41.2-4 bsdutils_1:2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b3 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-8 cpp-15-aarch64-linux-gnu_15.2.0-7cross1 cpp-15-x86-64-linux-gnu_15.2.0-8 cpp-aarch64-linux-gnu_4:15.2.0-4 cpp-x86-64-linux-gnu_4:15.2.0-4 crossbuild-essential-arm64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 fakeroot_1.37.1.2-1 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-8 g++-15-aarch64-linux-gnu_15.2.0-7cross1 g++-15-x86-64-linux-gnu_15.2.0-8 g++-aarch64-linux-gnu_4:15.2.0-4 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-8 gcc-15-aarch64-linux-gnu_15.2.0-7cross1 gcc-15-aarch64-linux-gnu-base_15.2.0-7cross1 gcc-15-base_15.2.0-8 gcc-15-cross-base_15.2.0-7cross1 gcc-15-x86-64-linux-gnu_15.2.0-8 gcc-aarch64-linux-gnu_4:15.2.0-4 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.12 libarchive-zip-perl_1.68-1 libasan8_15.2.0-8 libasan8-arm64-cross_15.2.0-7cross1 libatomic1_15.2.0-8 libatomic1-arm64-cross_15.2.0-7cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbamtools-dev_2.5.3+dfsg-1 libbamtools2.5.3_2.5.3+dfsg-1 libbinutils_2.45-8 libblkid1_2.41.2-4 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-arm64-cross_2.41-11cross1 libc6-dev_2.41-12 libc6-dev-arm64-cross_2.41-11cross1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-8 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45-8 libctf0_2.45-8 libcurl3t64-gnutls_8.17.0-2 libcurl4-gnutls-dev_8.17.0-2 libdb5.3t64_5.3.28+dfsg2-10 libdebconfclient0_0.281 libdebhelper-perl_13.28 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libelf1t64_0.194-1 libevent-2.1-7t64_2.1.12-stable-10+b1 libfakeroot_1.37.1.2-1 libfastahack-dev_1.0.0+dfsg-11+b2 libfastahack0_1.0.0+dfsg-11+b2 libffi8_3.5.2-2 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-8 libgcc-15-dev-arm64-cross_15.2.0-7cross1 libgcc-s1_15.2.0-8 libgcc-s1-arm64-cross_15.2.0-7cross1 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp-dev_2:6.3.0+dfsg-5 libgmp10_2:6.3.0+dfsg-5 libgmpxx4ldbl_2:6.3.0+dfsg-5 libgnutls-dane0t64_3.8.10-3 libgnutls-openssl27t64_3.8.10-3 libgnutls28-dev_3.8.10-3 libgnutls30t64_3.8.10-3 libgomp1_15.2.0-8 libgomp1-arm64-cross_15.2.0-7cross1 libgprofng0_2.45-8 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libgzstream-dev_1.5+git20171107.9a20658-3 libgzstream0_1.5+git20171107.9a20658-3 libhogweed6t64_3.10.2-1 libhts-dev_1.22.1+ds2-1 libhts3t64_1.22.1+ds2-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-8 libhwasan0-arm64-cross_15.2.0-7cross1 libidn2-0_2.3.8-4 libidn2-dev_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-8 libitm1-arm64-cross_15.2.0-7cross1 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libldap-dev_2.6.10+dfsg-1 libldap2_2.6.10+dfsg-1 liblsan0_15.2.0-8 liblsan0-arm64-cross_15.2.0-7cross1 liblz4-1_1.10.0-6 liblzma-dev_5.8.1-2 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncurses6_6.5+20250216-2 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp2-dev_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libnghttp3-dev_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-gnutls-dev_1.16.0-1 libngtcp2-crypto-gnutls8_1.16.0-1 libngtcp2-dev_1.16.0-1 libp11-kit-dev_0.25.9-2 libp11-kit0_0.25.9-2 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_10.46-1 libperl5.40_5.40.1-6 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_15.2.0-8 librtmp-dev_2.4+20151223.gitfa8646d.1-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2 libselinux1_3.9-2 libsemanage-common_3.9-1 libsemanage2_3.9-1 libsepol2_3.9-2 libsframe2_2.45-8 libsmartcols1_2.41.2-4 libsqlite3-0_3.46.1-8 libsqlite3-dev_3.46.1-8 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.4-1 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-8 libstdc++-15-dev-arm64-cross_15.2.0-7cross1 libstdc++6_15.2.0-8 libstdc++6-arm64-cross_15.2.0-7cross1 libsystemd0_258.1-2 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-7 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zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lumpy-sv Binary: lumpy-sv, lumpy-sv-examples Architecture: any all Version: 0.3.1+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/arq5x/lumpy-sv Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools Package-List: lumpy-sv deb science optional arch=any lumpy-sv-examples deb science optional arch=all Checksums-Sha1: b75a3ba46fb5197a96d8d5dccda356384c06bb77 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 4237faac649ff49f71fa9edac73689768ab3ad27 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz Checksums-Sha256: 78a6fe414739286d1f799bbdf3e34b9a1d6ed03b4c6dd17bfef1fcbba84bd35a 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 10a8ee20f04d1255322f09643940238685468d0f10e21cae7a046e834f2a4798 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz Files: 1167e4a94bceb29ac5b83cb170058e25 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 5876c8eaebf4fc93883197da876153eb 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaQPDMhIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtoUuAD/R0KPMsqdm9N4D9xaejuZx0ftADWl/KSm h/Ipw0wNjCkBAPOw9jQFwsfYCoKyq8D7whdRGE0xqfKdzh/aoNg90NMB =tEHJ -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting lumpy-sv in /<> dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying lumpyexpress.config.patch dpkg-source: info: applying fix_shebang.patch dpkg-source: info: applying do-not-override-dpkg-flags.patch dpkg-source: info: applying cleanup-bin.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.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.ziupjCUgyx/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-206f5638-da09-4893-8e93-42867b525a7f 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 lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra 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 '/<>' Cleaning up. make --no-print-directory -C src/filter/ clean rm -vf lumpy_filter #rm -Rf /lib #rm -f /src/api/*.o #rm -f /src/api/internal/*.o #rm -Rf /include 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 '/<>' [ -d bin ] || mkdir -p bin make --no-print-directory -C src/filter/ aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now cp src/filter/lumpy_filter bin [ -d bin ] || mkdir -p bin cp scripts/lumpyexpress bin/lumpyexpress > bin/lumpyexpress.config [ -d obj ] || mkdir -p obj [ -d bin ] || mkdir -p bin Building lumpy: ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ echo "- Building in $dir"; \ make --no-print-directory -C $dir; \ echo ""; \ done - Building in src/utils/bedFile * compiling bedFile.cpp In file included from bedFile.cpp:12: bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp In file included from bedFilePE.h:12, from bedFilePE.cpp:15: ../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 61 | long c2; | ^~ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * compiling BamAncillary.cpp In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ In file included from SV_Bedpe.h:19, from lumpy.cpp:27: SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ * compiling SV_Pair.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Pair.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_Evidence.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 81 | for (j = 0; j < size; ++j) { | ~~^~~~~~ * compiling SV_BreakPoint.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o In file included from SV_BreakPoint.h:19, from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_BreakPoint.cpp:1286:14: required from here 1286 | r_bin.add(interval_r.i.chr, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 1287 | interval_r.i.start, | ~~~~~~~~~~~~~~~~~~~ 1288 | interval_r.i.end, | ~~~~~~~~~~~~~~~~~ 1289 | interval_r.i.strand, | ~~~~~~~~~~~~~~~~~~~~ 1290 | this); | ~~~~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) | ~~~^~~~~~~~~ SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here 667 | unsigned int i, max_i; | ^~~~~ SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’: SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/15/cstdlib:83, from /usr/aarch64-linux-gnu/include/c++/15/bits/stl_algo.h:71, from /usr/aarch64-linux-gnu/include/c++/15/algorithm:63, from ../utils//UCSCBins/ucsc_bins.hpp:4: /usr/aarch64-linux-gnu/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/aarch64-linux-gnu/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ * compiling SV_Bedpe.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Bedpe.cpp:14: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:21, from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BedpeReader.h:22: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ * compiling SV_SplitRead.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); | ~~~~^~~~~~~~~~~~~~~~ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ * compiling SV_SplitReadReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * compiling SV_PairReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_BedpeReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Bedpe.h:18, from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_BedpeReader.h:23, from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ * compiling SV_BamReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] 208 | ( bam.Position < pos ) ) { | ~~~~~~~~~~~~~^~~~~ * compiling SV_InterChromBamReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * compiling SV_EvidenceReader.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o In file included from SV_EvidenceReader.h:20, from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_Tools.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o In file included from SV_Tools.h:19, from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_Tools.cpp:541:32: required from here 541 | exclude_regions.add(bed.chrom, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 542 | bed.start, | ~~~~~~~~~~ 543 | bed.end, | ~~~~~~~~ 544 | '+', | ~~~~ 545 | 1); | ~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_Tools.cpp:143:13: note: ‘last’ was declared here 143 | int last; | ^~~~ * compiling SV_VcfVariant.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling log_space.cpp aarch64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o * linking lumpy aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ -lz -L /<>/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/<>' cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam /bin/sh: 1: samtools: Exec format error make[1]: *** [debian/rules:20: override_dh_install] Error 126 make[1]: Leaving directory '/<>' make: *** [debian/rules:11: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2025-11-13T17:58:21Z +------------------------------------------------------------------------------+ | 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: 47 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 12 Job: lumpy-sv_0.3.1+dfsg-8 Machine Architecture: amd64 Package: lumpy-sv Package-Time: 70 Source-Version: 0.3.1+dfsg-8 Space: n/a Status: attempted Version: 0.3.1+dfsg-8 -------------------------------------------------------------------------------- Finished at 2025-11-13T17:58:21Z Build needed 00:01:10, no disk space