sbuild (Debian sbuild) 0.89.3+deb13u1 (16 August 2025) on mjolnir.einval.org +==============================================================================+ | lumpy-sv 0.3.1+dfsg-8 (amd64) Thu, 18 Dec 2025 14:07:28 +0000 | +==============================================================================+ Package: lumpy-sv Version: 0.3.1+dfsg-8 Source Version: 0.3.1+dfsg-8 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.SMWum1pooJ... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 18 Dec 2025 14:07:45 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [186 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.2 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.1 MB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [10.2 MB] Fetched 31.8 MB in 7s (4298 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: dpkg dpkg-dev libblkid1 libdpkg-perl libjansson4 libmount1 libsmartcols1 libuuid1 linux-libc-dev login util-linux zlib1g 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7937 kB of archives. After this operation, 203 kB disk space will be freed. Get:1 http://mirror.einval.org/debian unstable/main arm64 dpkg arm64 1.23.2 [1500 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libsmartcols1 arm64 2.41.3-1 [139 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libuuid1 arm64 2.41.3-1 [37.9 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libblkid1 arm64 2.41.3-1 [166 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libmount1 arm64 2.41.3-1 [199 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 util-linux arm64 2.41.3-1 [1124 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 login arm64 1:4.16.0-2+really2.41.3-1 [107 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg+really1.3.1-1+b2 [85.9 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 dpkg-dev all 1.23.2 [1317 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libdpkg-perl all 1.23.2 [658 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libjansson4 arm64 2.14-2+b4 [38.9 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 6.17.12-1 [2565 kB] Fetched 7937 kB in 0s (72.9 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12038 files and directories currently installed.) Preparing to unpack .../dpkg-dev_1.23.2_all.deb ... Unpacking dpkg-dev (1.23.2) over (1.22.21) ... Preparing to unpack .../libdpkg-perl_1.23.2_all.deb ... Unpacking libdpkg-perl (1.23.2) over (1.22.21) ... Preparing to unpack .../libjansson4_2.14-2+b4_arm64.deb ... Unpacking libjansson4:arm64 (2.14-2+b4) over (2.14-2+b3) ... Preparing to unpack .../linux-libc-dev_6.17.12-1_all.deb ... Unpacking linux-libc-dev (6.17.12-1) over (6.17.11-1) ... Setting up linux-libc-dev (6.17.12-1) ... Setting up libjansson4:arm64 (2.14-2+b4) ... Setting up libdpkg-perl (1.23.2) ... Setting up login (1:4.16.0-2+really2.41.3-1) ... Setting up dpkg-dev (1.23.2) ... Processing triggers for libc-bin (2.42-6) ... +------------------------------------------------------------------------------+ | Fetch source files Thu, 18 Dec 2025 14:08:06 +0000 | +------------------------------------------------------------------------------+ 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://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 0s (86.5 MB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 18 Dec 2025 14:08:09 +0000 | +------------------------------------------------------------------------------+ 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:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 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:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-UwX8vH/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ Sources [838 B] Get:5 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ Packages [881 B] Fetched 2328 B in 0s (106 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils comerr-dev:amd64 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbamtools-dev:amd64 libbamtools2.5.3:amd64 libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcrypt-dev:amd64 libcrypt1:amd64 libcurl3t64-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libfastahack-dev:amd64 libfastahack0:amd64 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls-openssl27t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libgzstream-dev:amd64 libgzstream0:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libncurses6:amd64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf3 libpsl-dev:amd64 libpsl5t64:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsqlite3-0:amd64 libsqlite3-dev:amd64 libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf samtools:amd64 sensible-utils zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc doc-base:amd64 gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc:amd64 libbamtools-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libcurl4-doc:amd64 libidn-dev:amd64 gmp-doc:amd64 libgmp10-doc:amd64 libmpfr-dev:amd64 dns-root-data:amd64 gnutls-bin:amd64 gnutls-doc:amd64 krb5-user:amd64 liblzma-doc:amd64 libnghttp2-doc:amd64 p11-kit-doc:amd64 sqlite3-doc:amd64 libssl-doc:amd64 libstdc++-15-doc:amd64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl cwltool:amd64 Recommended packages: curl | wget | lynx bzip2-doc:amd64 ca-certificates:amd64 libarchive-cpio-perl krb5-locales:amd64 libldap-common:amd64 libgpm2:amd64 publicsuffix:amd64 libsasl2-modules:amd64 libtasn1-doc:amd64 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils comerr-dev:amd64 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian krb5-multidev:amd64 libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbamtools-dev:amd64 libbamtools2.5.3:amd64 libbrotli-dev:amd64 libbrotli1:amd64 libbz2-1.0:amd64 libbz2-dev:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libcrypt-dev:amd64 libcrypt1:amd64 libcurl3t64-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3t64:amd64 libdebhelper-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1t64 libevent-2.1-7t64:amd64 libfastahack-dev:amd64 libfastahack0:amd64 libffi8:amd64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgmp-dev:amd64 libgmp10:amd64 libgmpxx4ldbl:amd64 libgnutls-dane0t64:amd64 libgnutls-openssl27t64:amd64 libgnutls28-dev:amd64 libgnutls30t64:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgssrpc4t64:amd64 libgzstream-dev:amd64 libgzstream0:amd64 libhogweed6t64:amd64 libhts-dev:amd64 libhts3t64:amd64 libhtscodecs2:amd64 libhwasan0:amd64 libhwasan0-amd64-cross libidn2-0:amd64 libidn2-dev:amd64 libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64 libkadm5clnt-mit12:amd64 libkadm5srv-mit12:amd64 libkdb5-10t64:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5-dev:amd64 libkrb5support0:amd64 libldap-dev:amd64 libldap2:amd64 liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1t64 libncurses6:amd64 libnettle8t64:amd64 libnghttp2-14:amd64 libnghttp2-dev:amd64 libnghttp3-9:amd64 libnghttp3-dev:amd64 libngtcp2-16:amd64 libngtcp2-crypto-gnutls-dev:amd64 libngtcp2-crypto-gnutls8:amd64 libngtcp2-dev:amd64 libp11-kit-dev:amd64 libp11-kit0:amd64 libpipeline1 libpkgconf3 libpsl-dev:amd64 libpsl5t64:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librtmp-dev:amd64 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libsqlite3-0:amd64 libsqlite3-dev:amd64 libssh2-1-dev:amd64 libssh2-1t64:amd64 libssl-dev:amd64 libssl3t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6:amd64 libtasn1-6-dev:amd64 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunbound8:amd64 libunistring5 libunistring5:amd64 libxml2-16 libzstd-dev:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db nettle-dev:amd64 pkgconf:amd64 pkgconf-bin po-debconf samtools:amd64 sbuild-build-depends-main-dummy:amd64 sensible-utils zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 160 newly installed, 0 to remove and 0 not upgraded. Need to get 130 MB of archives. After this operation, 513 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-UwX8vH/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.2-1 [242 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-10 [1130 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.3-1 [97.5 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-2 [40.3 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-3 [878 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.2-1 [772 kB] Get:17 http://mirror.einval.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-11 [53.9 kB] Get:18 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-11 [71.5 kB] Get:19 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-6 [1123 kB] Get:20 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.42-6 [1889 kB] Get:21 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Get:22 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.5.1-1 [128 kB] Get:23 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.42-6 [2090 kB] Get:24 http://mirror.einval.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b4 [25.1 kB] Get:25 http://mirror.einval.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b4 [56.7 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu-base arm64 15.2.0-7cross1 [53.5 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 cpp-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [11.3 MB] Get:28 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:15.2.0-4 [5296 B] Get:29 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.45.50.20251209-1 [1512 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-7cross1 [48.9 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 15.2.0-7cross1 [71.7 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 15.2.0-7cross1 [132 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 15.2.0-7cross1 [25.9 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 15.2.0-7cross1 [9228 B] Get:35 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 15.2.0-7cross1 [2770 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 15.2.0-7cross1 [1247 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 15.2.0-7cross1 [2479 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.42-4cross1 [1655 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 15.2.0-7cross1 [689 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 15.2.0-7cross1 [1106 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 15.2.0-7cross1 [1534 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 15.2.0-7cross1 [145 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-amd64-cross all 15.2.0-7cross1 [2706 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [21.8 MB] Get:45 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:15.2.0-4 [1448 B] Get:46 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.17.10-1cross1 [2401 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.42-4cross1 [2088 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-amd64-cross all 15.2.0-7cross1 [2423 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 g++-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [12.3 MB] Get:50 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:15.2.0-4 [1200 B] Get:51 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:52 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.29 [92.6 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-9 [540 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:58 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-2+b1 [591 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.2-1 [1613 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.29 [943 kB] Get:66 http://mirror.einval.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:67 http://mirror.einval.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:68 http://mirror.einval.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:69 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-2 [308 kB] Get:70 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b2 [89.0 kB] Get:71 http://mirror.einval.org/debian unstable/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Get:72 http://mirror.einval.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:73 http://mirror.einval.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-2 [60.3 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2 [42.5 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-2 [43.4 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-2 [56.2 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-2 [127 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 15.2.0-11 [2780 kB] Get:80 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-11 [9532 B] Get:81 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-11 [736 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libbamtools2.5.3 amd64 2.5.3+dfsg-1 [161 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b2 [919 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.3+dfsg-1 [221 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b9 [304 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b9 [316 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3 [26.1 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.10-1 [444 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.11-3 [1509 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get:106 http://mirror.einval.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:107 http://mirror.einval.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:108 http://mirror.einval.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:109 http://mirror.einval.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.18.0~rc2-1 [405 kB] Get:110 http://mirror.einval.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:111 http://mirror.einval.org/debian unstable/main amd64 libunbound8 amd64 1.24.2-1 [615 kB] Get:112 http://mirror.einval.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.11-3 [469 kB] Get:113 http://mirror.einval.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.11-3 [469 kB] Get:114 http://mirror.einval.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get:115 http://mirror.einval.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.10-1 [221 kB] Get:116 http://mirror.einval.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:117 http://mirror.einval.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get:118 http://mirror.einval.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get:119 http://mirror.einval.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1 [1322 kB] Get:120 http://mirror.einval.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.11-3 [1448 kB] Get:121 http://mirror.einval.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-2 [16.1 kB] Get:122 http://mirror.einval.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get:125 http://mirror.einval.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:126 http://mirror.einval.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get:127 http://mirror.einval.org/debian unstable/main amd64 libnghttp3-dev amd64 1.12.0-1 [95.5 kB] Get:128 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.16.0-1 [25.2 kB] Get:129 http://mirror.einval.org/debian unstable/main amd64 libngtcp2-dev amd64 1.16.0-1 [193 kB] Get:130 http://mirror.einval.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:131 http://mirror.einval.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get:132 http://mirror.einval.org/debian unstable/main amd64 libssl-dev amd64 3.5.4-1 [2980 kB] Get:133 http://mirror.einval.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:134 http://mirror.einval.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-2 [375 kB] Get:135 http://mirror.einval.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.18.0~rc2-1 [527 kB] Get:136 http://mirror.einval.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:137 http://mirror.einval.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:138 http://mirror.einval.org/debian unstable/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b2 [26.4 kB] Get:139 http://mirror.einval.org/debian unstable/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b2 [27.9 kB] Get:140 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-11 [140 kB] Get:141 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 15.2.0-11 [26.5 kB] Get:142 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-11 [1249 kB] Get:143 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-11 [2491 kB] Get:144 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-11 [1108 kB] Get:145 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-11 [1538 kB] Get:146 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-11 [145 kB] Get:147 http://mirror.einval.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-11 [2719 kB] Get:148 http://mirror.einval.org/debian unstable/main amd64 libgzstream0 amd64 1.5+git20171107.9a20658-3 [7032 B] Get:149 http://mirror.einval.org/debian unstable/main amd64 libgzstream-dev amd64 1.5+git20171107.9a20658-3 [7332 B] Get:150 http://mirror.einval.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:151 http://mirror.einval.org/debian unstable/main amd64 liblzma5 amd64 5.8.1-2 [310 kB] Get:152 http://mirror.einval.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get:153 http://mirror.einval.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get:154 http://mirror.einval.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1 [1807 kB] Get:155 http://mirror.einval.org/debian unstable/main amd64 libtinfo6 amd64 6.5+20251123-1 [353 kB] Get:156 http://mirror.einval.org/debian unstable/main amd64 libncurses6 amd64 6.5+20251123-1 [107 kB] Get:157 http://mirror.einval.org/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:158 http://mirror.einval.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-8 [1172 kB] Get:159 http://mirror.einval.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-11 [2444 kB] Get:160 http://mirror.einval.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Preconfiguring packages ... Fetched 130 MB in 2s (67.8 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 12026 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_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../002-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-gettext-base_0.23.2-1_arm64.deb ... Unpacking gettext-base (0.23.2-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../005-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../006-groff-base_1.23.0-10_arm64.deb ... Unpacking groff-base (1.23.0-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.41.3-1_arm64.deb ... Unpacking bsdextrautils (2.41.3-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../008-libpipeline1_1.5.8-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-2) ... Selecting previously unselected package man-db. Preparing to unpack .../009-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../010-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../011-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... 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Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-2+b1) ... Setting up libdebhelper-perl (13.29) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.2-1) ... Setting up m4 (1.4.20-2) ... Setting up gcc-15-x86-64-linux-gnu-base:arm64 (15.2.0-7cross1) ... Setting up file (1:5.46-5) ... Setting up cpp-15-x86-64-linux-gnu (15.2.0-7cross1) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.2-1) ... Setting up libc6-amd64-cross (2.42-4cross1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up gcc-15-cross-base (15.2.0-7cross1) ... Setting up libgcc-s1-amd64-cross (15.2.0-7cross1) ... Setting up gcc-15-base:amd64 (15.2.0-11) ... Setting up binutils-x86-64-linux-gnu (2.45.50.20251209-1) ... Setting up libstdc++6-amd64-cross (15.2.0-7cross1) ... Setting up cpp-x86-64-linux-gnu (4:15.2.0-4) ... Setting up automake (1:1.18.1-3) ... 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 gettext (0.23.2-1) ... Setting up libtool (2.5.4-9) ... Setting up libasan8-amd64-cross (15.2.0-7cross1) ... Setting up liblsan0-amd64-cross (15.2.0-7cross1) ... Setting up libc6-dev-amd64-cross (2.42-4cross1) ... Setting up libtsan2-amd64-cross (15.2.0-7cross1) ... Setting up libgomp1-amd64-cross (15.2.0-7cross1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libitm1-amd64-cross (15.2.0-7cross1) ... Setting up libatomic1-amd64-cross (15.2.0-7cross1) ... Setting up libhwasan0-amd64-cross (15.2.0-7cross1) ... Setting up libquadmath0-amd64-cross (15.2.0-7cross1) ... Setting up libubsan1-amd64-cross (15.2.0-7cross1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-15-dev-amd64-cross (15.2.0-7cross1) ... Setting up libstdc++-15-dev-amd64-cross (15.2.0-7cross1) ... Setting up debhelper (13.29) ... Setting up gcc-15-x86-64-linux-gnu (15.2.0-7cross1) ... Setting up g++-15-x86-64-linux-gnu (15.2.0-7cross1) ... Setting up gcc-x86-64-linux-gnu (4:15.2.0-4) ... Setting up g++-x86-64-linux-gnu (4:15.2.0-4) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (15.2.0-11) ... Setting up libc6:amd64 (2.42-6) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libnghttp3-dev:amd64 (1.12.0-1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-11) ... Setting up libffi8:amd64 (3.5.2-3) ... Setting up libhwasan0:amd64 (15.2.0-11) ... Setting up libasan8:amd64 (15.2.0-11) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libtsan2:amd64 (15.2.0-11) ... Setting up libbz2-1.0:amd64 (1.0.8-6) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libstdc++6:amd64 (15.2.0-11) ... Setting up liblsan0:amd64 (15.2.0-11) ... Setting up libitm1:amd64 (15.2.0-11) ... Setting up libtinfo6:amd64 (6.5+20251123-1) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up libzstd1:amd64 (1.5.7+dfsg-2) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-2) ... Setting up liblzma5:amd64 (5.8.1-2) ... Setting up libbrotli1:amd64 (1.1.0-2+b9) ... Setting up libsqlite3-0:amd64 (3.46.1-8) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.1-1+b2) ... Setting up libcrypt1:amd64 (1:4.5.1-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b4) ... Setting up libngtcp2-dev:amd64 (1.16.0-1) ... Setting up libgomp1:amd64 (15.2.0-11) ... Setting up libfastahack0:amd64 (1.0.0+dfsg-11+b2) ... Setting up libkrb5support0:amd64 (1.22.1-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Setting up libfastahack-dev:amd64 (1.0.0+dfsg-11+b2) ... Setting up libnettle8t64:amd64 (3.10.2-1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-5) ... Setting up libncurses6:amd64 (6.5+20251123-1) ... Setting up libquadmath0:amd64 (15.2.0-11) ... Setting up libp11-kit0:amd64 (0.25.10-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libatomic1:amd64 (15.2.0-11) ... Setting up libk5crypto3:amd64 (1.22.1-2) ... Setting up libgzstream0:amd64 (1.5+git20171107.9a20658-3) ... Setting up liblzma-dev:amd64 (5.8.1-2) ... Setting up libubsan1:amd64 (15.2.0-11) ... Setting up libbamtools2.5.3:amd64 (2.5.3+dfsg-1) ... Setting up libhogweed6t64:amd64 (3.10.2-1) ... Setting up libcrypt-dev:amd64 (1:4.5.1-1) ... Setting up libc6-dev:amd64 (2.42-6) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b9) ... Setting up libp11-kit-dev:amd64 (0.25.10-1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libgcc-15-dev:amd64 (15.2.0-11) ... Setting up libssl3t64:amd64 (3.5.4-1) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libgzstream-dev:amd64 (1.5+git20171107.9a20658-3) ... Setting up libunbound8:amd64 (1.24.2-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up libstdc++-15-dev:amd64 (15.2.0-11) ... Setting up libsqlite3-dev:amd64 (3.46.1-8) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b4) ... Setting up libssl-dev:amd64 (3.5.4-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b2) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libgnutls30t64:amd64 (3.8.11-3) ... Setting up libgnutls-openssl27t64:amd64 (3.8.11-3) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.2-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.11-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libbamtools-dev:amd64 (2.5.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up libgnutls28-dev:amd64 (3.8.11-3) ... Setting up libcurl3t64-gnutls:amd64 (8.18.0~rc2-1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.16.0-1) ... Setting up libgssrpc4t64:amd64 (1.22.1-2) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-2) ... Setting up libkdb5-10t64:amd64 (1.22.1-2) ... Setting up samtools:amd64 (1.22.1-1) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-2) ... Setting up krb5-multidev:amd64 (1.22.1-2) ... Setting up libkrb5-dev:amd64 (1.22.1-2) ... Setting up libcurl4-gnutls-dev:amd64 (8.18.0~rc2-1) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (14) ... Processing triggers for libc-bin (2.42-6) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 18 Dec 2025 14:09:08 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Thu, 18 Dec 2025 14:09:09 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) Toolchain package versions: binutils_2.45.50.20251209-1 dpkg-dev_1.23.2 g++-15_15.2.0-11 gcc-15_15.2.0-11 libc6-dev_2.42-6 libstdc++-15-dev_15.2.0-11 libstdc++-15-dev-amd64-cross_15.2.0-7cross1 libstdc++6_15.2.0-11 libstdc++6-amd64-cross_15.2.0-7cross1 linux-libc-dev_6.17.12-1 Package versions: apt_3.1.12 apt-utils_3.1.12 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45.50.20251209-1 binutils-aarch64-linux-gnu_2.45.50.20251209-1 binutils-common_2.45.50.20251209-1 binutils-x86-64-linux-gnu_2.45.50.20251209-1 bsdextrautils_2.41.3-1 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b4 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-11 cpp-15-aarch64-linux-gnu_15.2.0-11 cpp-15-x86-64-linux-gnu_15.2.0-7cross1 cpp-aarch64-linux-gnu_4:15.2.0-4 cpp-x86-64-linux-gnu_4:15.2.0-4 crossbuild-essential-amd64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.29 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_1.23.2 dpkg-dev_1.23.2 dwz_0.16-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-11 g++-15-aarch64-linux-gnu_15.2.0-11 g++-15-x86-64-linux-gnu_15.2.0-7cross1 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_15.2.0-11 gcc-15-aarch64-linux-gnu_15.2.0-11 gcc-15-base_15.2.0-11 gcc-15-cross-base_15.2.0-7cross1 gcc-15-x86-64-linux-gnu_15.2.0-7cross1 gcc-15-x86-64-linux-gnu-base_15.2.0-7cross1 gcc-aarch64-linux-gnu_4:15.2.0-4 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-2 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.12 libarchive-zip-perl_1.68-1 libasan8_15.2.0-11 libasan8-amd64-cross_15.2.0-7cross1 libatomic1_15.2.0-11 libatomic1-amd64-cross_15.2.0-7cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbamtools-dev_2.5.3+dfsg-1 libbamtools2.5.3_2.5.3+dfsg-1 libbinutils_2.45.50.20251209-1 libblkid1_2.41.3-1 libbrotli-dev_1.1.0-2+b9 libbrotli1_1.1.0-2+b9 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.42-6 libc-dev-bin_2.42-6 libc-gconv-modules-extra_2.42-6 libc6_2.42-6 libc6-amd64-cross_2.42-4cross1 libc6-dev_2.42-6 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sensible-utils_0.0.26 sqv_1.3.0-5 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 util-linux_2.41.3-1 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b2 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b2 +------------------------------------------------------------------------------+ | Build Thu, 18 Dec 2025 14:09:09 +0000 | +------------------------------------------------------------------------------+ 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: missing OpenPGP keyrings dpkg-source: info: verifying ./lumpy-sv_0.3.1+dfsg-8.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting lumpy-sv in /build/reproducible-path/lumpy-sv-0.3.1+dfsg 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.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --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 x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j1 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' 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 '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin make --no-print-directory -C src/filter/ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -fcf-protection 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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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: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, | ^~~~~~~~~~~~~ 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: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); | ^~~~~~~~~~~~~ * compiling SV_Pair.cpp x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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/x86_64-linux-gnu/include/c++/15/cstdlib:83, from /usr/x86_64-linux-gnu/include/c++/15/bits/stl_algo.h:71, from /usr/x86_64-linux-gnu/include/c++/15/algorithm:63, from ../utils//UCSCBins/ucsc_bins.hpp:4: /usr/x86_64-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/x86_64-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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -fcf-protection -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 x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -fcf-protection -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' 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 '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' 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 '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' make: *** [debian/rules:11: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess failed with exit status 2 -------------------------------------------------------------------------------- Build finished at 2025-12-18T14:12:44Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands Thu, 18 Dec 2025 14:12:44 +0000 | +------------------------------------------------------------------------------+ rm -Rf /build/reproducible-path/lumpy-sv-0.3.1+dfsg/ ---------------------------------------------------- I: Finished running 'rm -Rf /build/reproducible-path/lumpy-sv-0.3.1+dfsg/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- +------------------------------------------------------------------------------+ | Cleanup Thu, 18 Dec 2025 14:12:45 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died with exit 2) +------------------------------------------------------------------------------+ | Summary Thu, 18 Dec 2025 14:12:49 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 207 Distribution: unstable Fail-Stage: build Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 59 Job: lumpy-sv_0.3.1+dfsg-8 Machine Architecture: arm64 Package: lumpy-sv Package-Time: 316 Source-Version: 0.3.1+dfsg-8 Space: n/a Status: attempted Version: 0.3.1+dfsg-8 -------------------------------------------------------------------------------- Finished at 2025-12-18T14:12:44Z Build needed 00:05:16, no disk space