sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir.einval.org +==============================================================================+ | freebayes 1.3.6-2 (amd64) Tue, 08 Nov 2022 02:41:53 +0000 | +==============================================================================+ Package: freebayes Version: 1.3.6-2 Source Version: 1.3.6-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-d6db17a9-9de2-47d5-b576-6f23ccaec07a' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-HjbrPv/resolver-TMJZUD' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [161 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main amd64 Packages [9388 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9980 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [9240 kB] Fetched 28.8 MB in 8s (3435 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: 'freebayes' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/freebayes.git Please use: git clone https://salsa.debian.org/med-team/freebayes.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2912 kB of source archives. Get:1 http://mirror.einval.org/debian sid/main freebayes 1.3.6-2 (dsc) [2232 B] Get:2 http://mirror.einval.org/debian sid/main freebayes 1.3.6-2 (tar) [2898 kB] Get:3 http://mirror.einval.org/debian sid/main freebayes 1.3.6-2 (diff) [11.4 kB] Fetched 2912 kB in 0s (25.2 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/freebayes-HjbrPv/freebayes-1.3.6' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-HjbrPv' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, debhelper, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, debhelper, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [511 B] Get:5 copy:/<>/apt_archive ./ Packages [578 B] Fetched 2046 B in 0s (46.1 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc binutils-x86-64-linux-gnu bsdextrautils cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbamtools-dev:amd64 libbamtools2.5.2:amd64 libbrotli1:amd64 libbwa-dev:amd64 libbz2-1.0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl3-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libdisorder-dev:amd64 libdisorder0:amd64 libelf1 libexpat1 libfastahack-dev:amd64 libfastahack0:amd64 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfml-dev:amd64 libfml0:amd64 libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu71 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjsoncpp-dev:amd64 libjsoncpp25:amd64 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.5-0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libmpdec3 libncurses6:amd64 libncursesw6 libnettle8:amd64 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpipeline1 libpsl5:amd64 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libseqlib-dev:amd64 libseqlib2:amd64 libsmithwaterman-dev:amd64 libsmithwaterman0:amd64 libsqlite3-0 libssh2-1:amd64 libssl3:amd64 libssw-dev:amd64 libssw0:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtabixpp-dev:amd64 libtabixpp0:amd64 libtasn1-6:amd64 libtinfo6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libvcflib-dev:amd64 libvcflib1:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types meson ninja-build pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.10 python3.10-minimal readline-common samtools:amd64 sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch g++-12-multilib-x86-64-linux-gnu gcc-12-doc gcc-12-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libcurl4-doc:amd64 libgnutls28-dev:amd64 libidn11-dev:amd64 libkrb5-dev:amd64 libldap2-dev:amd64 librtmp-dev:amd64 libssh2-1-dev:amd64 low-memory-monitor gnutls-bin:amd64 krb5-doc:amd64 krb5-user:amd64 liblzma-doc:amd64 libstdc++-12-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.10-venv python3.10-doc binfmt-support readline-doc cwltool:amd64 Recommended packages: curl | wget | lynx ca-certificates:amd64 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales:amd64 libldap-common:amd64 libgpm2:amd64 libgpm2 publicsuffix:amd64 libsasl2-modules:amd64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc binutils-x86-64-linux-gnu bsdextrautils cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libbamtools-dev:amd64 libbamtools2.5.2:amd64 libbrotli1:amd64 libbwa-dev:amd64 libbz2-1.0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl3-gnutls:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libdisorder-dev:amd64 libdisorder0:amd64 libelf1 libexpat1 libfastahack-dev:amd64 libfastahack0:amd64 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfml-dev:amd64 libfml0:amd64 libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu71 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjsoncpp-dev:amd64 libjsoncpp25:amd64 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.5-0:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libmpdec3 libncurses6:amd64 libncursesw6 libnettle8:amd64 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpipeline1 libpsl5:amd64 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 librtmp1:amd64 libsasl2-2:amd64 libsasl2-modules-db:amd64 libseqlib-dev:amd64 libseqlib2:amd64 libsmithwaterman-dev:amd64 libsmithwaterman0:amd64 libsqlite3-0 libssh2-1:amd64 libssl3:amd64 libssw-dev:amd64 libssw0:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtabixpp-dev:amd64 libtabixpp0:amd64 libtasn1-6:amd64 libtinfo6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libvcflib-dev:amd64 libvcflib1:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types meson ninja-build pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.10 python3.10-minimal readline-common samtools:amd64 sbuild-build-depends-main-dummy:amd64 sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 179 newly installed, 0 to remove and 0 not upgraded. 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0.0.7-1 [67.9 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-8 [882 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.38.1-1.1+b1 [86.3 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.6-3 [37.4 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.11.0-1+b1 [1324 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.19-1 [280 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-9 [510 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 bc arm64 1.07.1-3 [107 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 gcc-12-x86-64-linux-gnu-base arm64 12.2.0-9cross2 [37.3 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 cpp-12-x86-64-linux-gnu arm64 12.2.0-9cross2 [8767 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:12.2.0-1 [17.1 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.39-8 [2339 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 gcc-12-cross-base all 12.2.0-9cross2 [32.8 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-amd64-cross all 12.2.0-9cross2 [49.9 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libgomp1-amd64-cross all 12.2.0-9cross2 [113 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 12.2.0-9cross2 [25.6 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 12.2.0-9cross2 [9064 B] Get:44 http://mirror.einval.org/debian sid/main arm64 libasan8-amd64-cross all 12.2.0-9cross2 [2193 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 liblsan0-amd64-cross all 12.2.0-9cross2 [968 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libtsan2-amd64-cross all 12.2.0-9cross2 [2197 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.36-3cross1 [1473 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libstdc++6-amd64-cross all 12.2.0-9cross2 [569 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libubsan1-amd64-cross all 12.2.0-9cross2 [882 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libquadmath0-amd64-cross all 12.2.0-9cross2 [144 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libgcc-12-dev-amd64-cross all 12.2.0-9cross2 [2436 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 gcc-12-x86-64-linux-gnu arm64 12.2.0-9cross2 [17.4 MB] Get:53 http://mirror.einval.org/debian sid/main arm64 gcc-x86-64-linux-gnu arm64 4:12.2.0-1 [1452 B] Get:54 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 6.0.6-2cross1 [1803 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.36-3cross1 [1890 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libstdc++-12-dev-amd64-cross all 12.2.0-9cross2 [2027 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 g++-12-x86-64-linux-gnu arm64 12.2.0-9cross2 [9598 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:12.2.0-1 [1176 B] Get:59 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libicu71 arm64 71.1-3 [9046 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.14+dfsg-1.1 [619 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b1 [309 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-2 [63.4 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:75 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.10.1 [79.9 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.7-4 [526 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get:80 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.187-4 [179 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14+20220924-2 [101 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-9 [1262 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.10.1 [940 kB] Get:88 http://mirror.einval.org/debian sid/main amd64 gcc-12-base amd64 12.2.0-9 [37.0 kB] Get:89 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 12.2.0-9 [49.9 kB] Get:90 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.36-4 [2747 kB] Get:91 http://mirror.einval.org/debian sid/main amd64 libasan8 amd64 12.2.0-9 [2193 kB] Get:92 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 12.2.0-9 [9328 B] Get:93 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 12.2.0-9 [614 kB] Get:94 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:95 http://mirror.einval.org/debian sid/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-2 [150 kB] Get:96 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 6.0.7-1 [1677 kB] Get:97 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.30-1 [89.0 kB] Get:98 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.30-1 [118 kB] Get:99 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.6~rc1-1+b1 [14.8 kB] Get:100 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.20-1+b1 [32.2 kB] Get:101 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.20-1+b1 [78.6 kB] Get:102 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:103 http://mirror.einval.org/debian sid/main amd64 libssl3 amd64 3.0.7-1 [2008 kB] Get:104 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.20-1+b1 [331 kB] Get:105 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20-1+b1 [133 kB] Get:106 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:107 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:108 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:109 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:110 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.36-4 [1895 kB] Get:111 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:112 http://mirror.einval.org/debian sid/main amd64 libbamtools-dev amd64 2.5.2+dfsg-2 [215 kB] Get:113 http://mirror.einval.org/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b4 [275 kB] Get:114 http://mirror.einval.org/debian sid/main amd64 libbwa-dev amd64 0.7.17-7 [156 kB] Get:115 http://mirror.einval.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:116 http://mirror.einval.org/debian sid/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:117 http://mirror.einval.org/debian sid/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:118 http://mirror.einval.org/debian sid/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:119 http://mirror.einval.org/debian sid/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:120 http://mirror.einval.org/debian sid/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:121 http://mirror.einval.org/debian sid/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:122 http://mirror.einval.org/debian sid/main amd64 libp11-kit0 amd64 0.24.1-1 [352 kB] Get:123 http://mirror.einval.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:124 http://mirror.einval.org/debian sid/main amd64 libgnutls30 amd64 3.7.8-4 [1389 kB] Get:125 http://mirror.einval.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.10 [687 kB] Get:126 http://mirror.einval.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-8 [38.7 kB] Get:127 http://mirror.einval.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg-8 [78.2 kB] Get:128 http://mirror.einval.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-2+b1 [183 kB] Get:129 http://mirror.einval.org/debian sid/main amd64 libnghttp2-14 amd64 1.50.0-1+b1 [73.1 kB] Get:130 http://mirror.einval.org/debian sid/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:131 http://mirror.einval.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:132 http://mirror.einval.org/debian sid/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:133 http://mirror.einval.org/debian sid/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [275 kB] Get:134 http://mirror.einval.org/debian sid/main amd64 libcurl3-gnutls amd64 7.86.0-1 [358 kB] Get:135 http://mirror.einval.org/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.86.0-1 [454 kB] Get:136 http://mirror.einval.org/debian sid/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:137 http://mirror.einval.org/debian sid/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get:138 http://mirror.einval.org/debian sid/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B] Get:139 http://mirror.einval.org/debian sid/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b1 [4860 B] Get:140 http://mirror.einval.org/debian sid/main amd64 libfastahack0 amd64 1.0.0+dfsg-10 [25.7 kB] Get:141 http://mirror.einval.org/debian sid/main amd64 libfastahack-dev amd64 1.0.0+dfsg-10 [27.0 kB] Get:142 http://mirror.einval.org/debian sid/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB] Get:143 http://mirror.einval.org/debian sid/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB] Get:144 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 12.2.0-9 [116 kB] Get:145 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 12.2.0-9 [26.1 kB] Get:146 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 12.2.0-9 [969 kB] Get:147 http://mirror.einval.org/debian sid/main amd64 libtsan2 amd64 12.2.0-9 [2197 kB] Get:148 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 12.2.0-9 [883 kB] Get:149 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 12.2.0-9 [145 kB] Get:150 http://mirror.einval.org/debian sid/main amd64 libgcc-12-dev amd64 12.2.0-9 [2436 kB] Get:151 http://mirror.einval.org/debian sid/main arm64 libglib2.0-0 arm64 2.74.1-1 [1324 kB] Get:152 http://mirror.einval.org/debian sid/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:153 http://mirror.einval.org/debian sid/main amd64 liblzma5 amd64 5.2.7-0.1 [181 kB] Get:154 http://mirror.einval.org/debian sid/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:155 http://mirror.einval.org/debian sid/main amd64 liblzma-dev amd64 5.2.7-0.1 [239 kB] Get:156 http://mirror.einval.org/debian sid/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get:157 http://mirror.einval.org/debian sid/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get:158 http://mirror.einval.org/debian sid/main amd64 libjsoncpp-dev amd64 1.9.5-4 [26.4 kB] Get:159 http://mirror.einval.org/debian sid/main amd64 libtinfo6 amd64 6.3+20220423-2 [351 kB] Get:160 http://mirror.einval.org/debian sid/main amd64 libncurses6 amd64 6.3+20220423-2 [102 kB] Get:161 http://mirror.einval.org/debian sid/main amd64 libssw0 amd64 1.1-13 [19.7 kB] Get:162 http://mirror.einval.org/debian sid/main amd64 libseqlib2 amd64 1.2.0+dfsg-9 [162 kB] Get:163 http://mirror.einval.org/debian sid/main amd64 libssw-dev amd64 1.1-13 [22.4 kB] Get:164 http://mirror.einval.org/debian sid/main amd64 libseqlib-dev amd64 1.2.0+dfsg-9 [209 kB] Get:165 http://mirror.einval.org/debian sid/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get:166 http://mirror.einval.org/debian sid/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB] Get:167 http://mirror.einval.org/debian sid/main amd64 libstdc++-12-dev amd64 12.2.0-9 [2047 kB] Get:168 http://mirror.einval.org/debian sid/main amd64 libtabixpp0 amd64 1.1.1-1 [9580 B] Get:169 http://mirror.einval.org/debian sid/main amd64 libtabixpp-dev amd64 1.1.1-1 [8640 B] Get:170 http://mirror.einval.org/debian sid/main amd64 libvcflib1 amd64 1.0.3+dfsg-2 [153 kB] Get:171 http://mirror.einval.org/debian sid/main amd64 libvcflib-dev amd64 1.0.3+dfsg-2 [85.2 kB] Get:172 http://mirror.einval.org/debian sid/main arm64 ninja-build arm64 1.11.1-1 [127 kB] Get:173 http://mirror.einval.org/debian sid/main arm64 python3-pkg-resources all 65.5.0-1 [278 kB] Get:174 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.10.8-1 [77.3 kB] Get:175 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.10.8-1 [139 kB] Get:176 http://mirror.einval.org/debian sid/main arm64 python3-setuptools all 65.5.0-1 [519 kB] Get:177 http://mirror.einval.org/debian sid/main arm64 meson all 0.64.0-1 [542 kB] Get:178 http://mirror.einval.org/debian sid/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get:179 http://mirror.einval.org/debian sid/main amd64 samtools amd64 1.16.1-1 [607 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 117 MB in 2s (53.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12609 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4+b3_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b3) ... Selecting previously unselected package libpython3.10-minimal:arm64. Preparing to unpack .../libpython3.10-minimal_3.10.8-3_arm64.deb ... Unpacking libpython3.10-minimal:arm64 (3.10.8-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.8-3_arm64.deb ... Unpacking python3.10-minimal (3.10.8-3) ... Setting up libpython3.10-minimal:arm64 (3.10.8-3) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.10-minimal (3.10.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 12929 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.10.6-1_arm64.deb ... Unpacking python3-minimal (3.10.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_8.0.0_all.deb ... Unpacking media-types (8.0.0) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../2-libmpdec3_2.5.1-2_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-2) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../3-libncursesw6_6.3+20220423-2_arm64.deb ... Unpacking libncursesw6:arm64 (6.3+20220423-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.1_all.deb ... Unpacking readline-common (8.2-1.1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../5-libreadline8_8.2-1.1_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.1) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../6-libsqlite3-0_3.39.4-1_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.39.4-1) ... Selecting previously unselected package libpython3.10-stdlib:arm64. Preparing to unpack .../7-libpython3.10-stdlib_3.10.8-3_arm64.deb ... Unpacking libpython3.10-stdlib:arm64 (3.10.8-3) ... Selecting previously unselected package python3.10. Preparing to unpack .../8-python3.10_3.10.8-3_arm64.deb ... Unpacking python3.10 (3.10.8-3) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.10.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.10.6-1) ... Setting up python3-minimal (3.10.6-1) ... Selecting previously unselected package python3. (Reading database ... 13372 files and directories currently installed.) Preparing to unpack .../000-python3_3.10.6-1_arm64.deb ... Unpacking python3 (3.10.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.41-4_arm64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../003-libmagic1_1%3a5.41-4_arm64.deb ... Unpacking libmagic1:arm64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.41-4_arm64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-9_arm64.deb ... Unpacking gettext-base (0.21-9) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.22.4-8_arm64.deb ... Unpacking groff-base (1.22.4-8) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.38.1-1.1+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-1.1+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.6-3_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.6-3) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.11.0-1+b1_arm64.deb ... Unpacking man-db (2.11.0-1+b1) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-1_arm64.deb ... Unpacking m4 (1.4.19-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. 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Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-8) ... Setting up libpython3-stdlib:arm64 (3.10.6-1) ... Setting up libgcc-12-dev-amd64-cross (12.2.0-9cross2) ... Setting up python3.10 (3.10.8-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.10.6-1) ... Setting up libstdc++-12-dev-amd64-cross (12.2.0-9cross2) ... Setting up man-db (2.11.0-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-12-x86-64-linux-gnu (12.2.0-9cross2) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up python3-pkg-resources (65.5.0-1) ... Setting up python3-distutils (3.10.8-1) ... Setting up python3-setuptools (65.5.0-1) ... Setting up gcc-x86-64-linux-gnu (4:12.2.0-1) ... Setting up meson (0.64.0-1) ... Setting up debhelper (13.10.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-12-x86-64-linux-gnu (12.2.0-9cross2) ... Setting up libconfig-auto-perl (0.44-2) ... 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Processing triggers for libc-bin (2.36-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-0.bpo.15-arm64 #1 SMP Debian 5.10.120-1~bpo10+1 (2022-06-13) arm64 (aarch64) Toolchain package versions: binutils_2.39-8 dpkg-dev_1.21.9 g++-12_12.2.0-9 gcc-12_12.2.0-9 libc6-dev_2.36-4 libstdc++-12-dev_12.2.0-9 libstdc++-12-dev-amd64-cross_12.2.0-9cross2 libstdc++6_12.2.0-9 libstdc++6-amd64-cross_12.2.0-9cross2 linux-libc-dev_6.0.7-1 Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2-2+b1 bc_1.07.1-3 binutils_2.39-8 binutils-aarch64-linux-gnu_2.39-8 binutils-common_2.39-8 binutils-x86-64-linux-gnu_2.39-8 bsdextrautils_2.38.1-1.1+b1 bsdutils_1:2.38.1-1.1+b1 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-1 cpp-12_12.2.0-9 cpp-12-x86-64-linux-gnu_12.2.0-9cross2 cpp-x86-64-linux-gnu_4:12.2.0-1 cross-config_2.6.18+nmu2 crossbuild-essential-amd64_12.9 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debian-archive-keyring_2021.1.1 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dpkg_1.21.9+b1 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.9 dwz_0.14+20220924-2 fakeroot_1.30.1-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1 g++-12_12.2.0-9 g++-12-x86-64-linux-gnu_12.2.0-9cross2 g++-x86-64-linux-gnu_4:12.2.0-1 gcc_4:12.2.0-1 gcc-12_12.2.0-9 gcc-12-base_12.2.0-9 gcc-12-cross-base_12.2.0-9cross2 gcc-12-x86-64-linux-gnu_12.2.0-9cross2 gcc-12-x86-64-linux-gnu-base_12.2.0-9cross2 gcc-x86-64-linux-gnu_4:12.2.0-1 gettext_0.21-9 gettext-base_0.21-9 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-1 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libasan8_12.2.0-9 libasan8-amd64-cross_12.2.0-9cross2 libatomic1_12.2.0-9 libatomic1-amd64-cross_12.2.0-9cross2 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1+b1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.39-8 libblkid1_2.38.1-1.1+b1 libbrotli1_1.0.9-2+b4 libbwa-dev_0.7.17-7 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-4 libc-dev-bin_2.36-4 libc6_2.36-4 libc6-amd64-cross_2.36-3cross1 libc6-dev_2.36-4 libc6-dev-amd64-cross_2.36-3cross1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.44-1 libcc1-0_12.2.0-9 libcom-err2_1.46.6~rc1-1+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.30-1 libcrypt1_1:4.4.30-1 libctf-nobfd0_2.39-8 libctf0_2.39-8 libcurl3-gnutls_7.86.0-1 libcurl4-gnutls-dev_7.86.0-1 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libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.8-3 libpython3.10-stdlib_3.10.8-3 libquadmath0_12.2.0-9 libquadmath0-amd64-cross_12.2.0-9cross2 libreadline8_8.2-1.1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+b1 libselinux1_3.4-1+b2 libsemanage-common_3.4-1 libsemanage2_3.4-1+b2 libsepol2_3.4-2 libseqlib-dev_1.2.0+dfsg-9 libseqlib2_1.2.0+dfsg-9 libsmartcols1_2.38.1-1.1+b1 libsmithwaterman-dev_0.0+git20160702.2610e25-12+b1 libsmithwaterman0_0.0+git20160702.2610e25-12+b1 libsqlite3-0_3.39.4-1 libssh2-1_1.10.0-3+b1 libssl3_3.0.7-1 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-12-dev_12.2.0-9 libstdc++-12-dev-amd64-cross_12.2.0-9cross2 libstdc++6_12.2.0-9 libstdc++6-amd64-cross_12.2.0-9cross2 libsub-override-perl_0.09-4 libsystemd0_252-3 libtabixpp-dev_1.1.1-1 libtabixpp0_1.1.1-1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libtsan2_12.2.0-9 libtsan2-amd64-cross_12.2.0-9cross2 libubsan1_12.2.0-9 libubsan1-amd64-cross_12.2.0-9cross2 libuchardet0_0.0.7-1 libudev1_252-3 libunistring2_1.0-2 libuuid1_2.38.1-1.1+b1 libvcflib-dev_1.0.3+dfsg-2 libvcflib1_1.0.3+dfsg-2 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libyaml-perl_1.30-2 libzstd1_1.5.2+dfsg-1 linux-libc-dev_6.0.7-1 linux-libc-dev-amd64-cross_6.0.6-2cross1 login_1:4.12.3+dfsg1-3 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1+b1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 meson_0.64.0-1 mount_2.38.1-1.1+b1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ninja-build_1.11.1-1 passwd_1:4.12.3+dfsg1-3 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.36_5.36.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-distutils_3.10.8-1 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1 python3-pkg-resources_65.5.0-1 python3-setuptools_65.5.0-1 python3.10_3.10.8-3 python3.10-minimal_3.10.8-3 readline-common_8.2-1.1 rpcsvc-proto_1.4.2-4 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022f-1 ucf_3.0043 usrmerge_33 util-linux_2.38.1-1.1+b1 util-linux-extra_2.38.1-1.1+b1 xz-utils_5.2.7-0.1 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: freebayes Binary: freebayes Architecture: any Version: 1.3.6-2 Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/freebayes Vcs-Git: https://salsa.debian.org/med-team/freebayes.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel , libvcflib-tools , debhelper Package-List: freebayes deb science optional arch=any Checksums-Sha1: 2513323e336e02b5cc83d43c9f5b725579c0b75a 2898209 freebayes_1.3.6.orig.tar.gz 504b332ace3ff066468126e5559e058877bdfa0c 11440 freebayes_1.3.6-2.debian.tar.xz Checksums-Sha256: d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 2898209 freebayes_1.3.6.orig.tar.gz 2fbada9aaa038dc048d99a28e91201f4b57f240a5119fd01e83bdf3224e63872 11440 freebayes_1.3.6-2.debian.tar.xz Files: e8fe2bf8bb0139bb313744e5fb8e4105 2898209 freebayes_1.3.6.orig.tar.gz cd9f68ade2865de3a9d15cab4fce73fe 11440 freebayes_1.3.6-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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13:45:15 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./freebayes_1.3.6-2.dsc dpkg-source: info: extracting freebayes in /<> dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.6-2.debian.tar.xz Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- 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=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-d6db17a9-9de2-47d5-b576-6f23ccaec07a SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.6-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary-arch dh binary-arch --buildsystem=meson --builddir=build dh_update_autotools_config -a -O--buildsystem=meson -O--builddir=build dh_autoreconf -a -O--buildsystem=meson -O--builddir=build dh_auto_configure -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu --cross-file /<>/debian/.debhelper/generated/_source/meson-cross-file.conf DEPRECATION: c_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: cpp_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: c_link_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. DEPRECATION: cpp_link_args in the [properties] section of the machine file is deprecated, use the [built-in options] section. The Meson build system Version: 0.64.0 Source dir: /<> Build dir: /<>/build Build type: cross build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: /usr/bin/x86_64-linux-gnu-gcc (gcc 12.2.0 "x86_64-linux-gnu-gcc (Debian 12.2.0-9) 12.2.0") C linker for the host machine: /usr/bin/x86_64-linux-gnu-gcc ld.bfd 2.39 C++ compiler for the host machine: /usr/bin/x86_64-linux-gnu-g++ (gcc 12.2.0 "x86_64-linux-gnu-g++ (Debian 12.2.0-9) 12.2.0") C++ linker for the host machine: /usr/bin/x86_64-linux-gnu-g++ ld.bfd 2.39 C compiler for the build machine: cc (gcc 12.2.0 "cc (Debian 12.2.0-9) 12.2.0") C linker for the build machine: cc ld.bfd 2.39 C++ compiler for the build machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-9) 12.2.0") C++ linker for the build machine: c++ ld.bfd 2.39 Build machine cpu family: aarch64 Build machine cpu: aarch64 Host machine cpu family: x86_64 Host machine cpu: amd64 Target machine cpu family: x86_64 Target machine cpu: amd64 Found pkg-config: /usr/bin/x86_64-linux-gnu-pkg-config (0.29.2) Run-time dependency zlib found: YES 1.2.13 Run-time dependency liblzma found: YES 5.2.7 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.16 Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 freebayes 1.3.6 User defined options Cross files : /<>/debian/.debhelper/generated/_source/meson-cross-file.conf buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir: /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload Found ninja-1.11.1 at /usr/bin/ninja WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated. dh_auto_build -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j1 -v [1/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp ../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] 160 | switch (this->type) { | ^ ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] [2/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp In file included from ../src/AlleleParser.h:32, from ../src/AlleleParser.cpp:1: /usr/include/vcflib/Variant.h:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/ostream:38, from /usr/x86_64-linux-gnu/include/c++/12/iostream:39, from ../src/AlleleParser.h:4: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [3/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [4/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [5/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [6/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [7/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp In file included from ../src/AlleleParser.h:32, from ../src/DataLikelihood.h:20, from ../src/DataLikelihood.cpp:1: /usr/include/vcflib/Variant.h:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/ostream:38, from /usr/x86_64-linux-gnu/include/c++/12/iostream:39, from ../src/DataLikelihood.h:4: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [8/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [9/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [10/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp ../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSequence(std::string)’: ../src/FBFasta.cpp:273:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free] 273 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:272:9: note: call to ‘void free(void*)’ here 272 | free(seq); | ~~~~^~~~~ ../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSubSequence(std::string, int, int)’: ../src/FBFasta.cpp:316:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free] 316 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here 315 | free(seq); | ~~~~^~~~~ [11/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp [12/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [13/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [14/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/Marginals.h:7, from ../src/Marginals.cpp:1: /usr/include/vcflib/Variant.h:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/refwrap.h:39, from /usr/x86_64-linux-gnu/include/c++/12/vector:66, from ../src/Marginals.h:4: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [15/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [16/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [17/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [18/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [19/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/ResultData.cpp:1: /usr/include/vcflib/Variant.h:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/refwrap.h:39, from /usr/x86_64-linux-gnu/include/c++/12/vector:66, from ../src/ResultData.h:4: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [20/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [21/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [22/27] /usr/bin/x86_64-linux-gnu-g++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with long unsigned int value_size = 1]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[0]))’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[2]))’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt& ttmath::UInt::operator=(const ttmath::UInt&) [with long unsigned int value_size = 1]’, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[0]))’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::uint ttmath::Int::FromUIntOrInt(const ttmath::UInt&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’, inlined from ‘ttmath::uint ttmath::Int::FromInt(const ttmath::Int&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23, inlined from ‘ttmath::Int& ttmath::Int::operator=(const ttmath::Int&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10, inlined from ‘ttmath::Big& ttmath::Big::operator=(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12, inlined from ‘ttmath::Big::Big(const ttmath::Big&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12, inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9, inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44: ../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::.ttmath::UInt<4>::table[2]))’ may be used uninitialized [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [23/27] rm -f libfreebayes_common.a && /usr/bin/x86_64-linux-gnu-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [24/27] /usr/bin/x86_64-linux-gnu-g++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp In file included from ../src/AlleleParser.h:32, from ../src/freebayes.cpp:29: /usr/include/vcflib/Variant.h:651:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/ostream:38, from /usr/x86_64-linux-gnu/include/c++/12/iostream:39, from ../src/freebayes.cpp:9: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:652:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [25/27] /usr/bin/x86_64-linux-gnu-g++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /lib/x86_64-linux-gnu/libtabixpp.so /lib/x86_64-linux-gnu/libvcflib.so /lib/x86_64-linux-gnu/libsmithwaterman.so /lib/x86_64-linux-gnu/libdisorder.so /lib/x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group [26/27] /usr/bin/x86_64-linux-gnu-g++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [27/27] /usr/bin/x86_64-linux-gnu-g++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /lib/x86_64-linux-gnu/libvcflib.so /lib/x86_64-linux-gnu/libsmithwaterman.so /lib/x86_64-linux-gnu/libdisorder.so /lib/x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /lib/x86_64-linux-gnu/libtabixpp.so -Wl,--end-group create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson -O--builddir=build dh_prep -a -O--buildsystem=meson -O--builddir=build dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/<>/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /<>/debian/freebayes/usr/bin Installing bamleftalign to /<>/debian/freebayes/usr/bin dh_install -a -O--buildsystem=meson -O--builddir=build dh_installdocs -a -O--buildsystem=meson -O--builddir=build dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build dh_installexamples -a -O--buildsystem=meson -O--builddir=build dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build dh_perl -a -O--buildsystem=meson -O--builddir=build dh_link -a -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build dh_compress -a -O--buildsystem=meson -O--builddir=build dh_fixperms -a -O--buildsystem=meson -O--builddir=build dh_missing -a -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dh_installdeb -a -O--buildsystem=meson -O--builddir=build dh_gencontrol -a -O--buildsystem=meson -O--builddir=build dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a -O--buildsystem=meson -O--builddir=build dh_builddeb -a -O--buildsystem=meson -O--builddir=build dpkg-deb: building package 'freebayes' in '../freebayes_1.3.6-2_amd64.deb'. dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.6-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../freebayes_1.3.6-2_amd64.buildinfo dpkg-genchanges --build=any -O../freebayes_1.3.6-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-11-08T02:50:25Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.6-2_amd64.changes: -------------------------------- Format: 1.8 Date: Tue, 01 Nov 2022 14:38:51 +0100 Source: freebayes Binary: freebayes freebayes-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 1.3.6-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.6-2) unstable; urgency=medium . * install scripts (+ python3 dependency accordingly) * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: d5fc80330f3540c4dc501c1171a0c0b8455dd303 6576592 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freebayes Binary: freebayes freebayes-dbgsym Architecture: amd64 Version: 1.3.6-2 Checksums-Md5: a453c32f370c416908422d1feb0feea7 6576592 freebayes-dbgsym_1.3.6-2_amd64.deb 2e2c8da210a64be7f3ddb81e3455ebde 1469624 freebayes_1.3.6-2_amd64.deb Checksums-Sha1: d5fc80330f3540c4dc501c1171a0c0b8455dd303 6576592 freebayes-dbgsym_1.3.6-2_amd64.deb b882967767b6d74acf117b3f1b8dc1df13003333 1469624 freebayes_1.3.6-2_amd64.deb Checksums-Sha256: 99712783d9f3dbf734175f387140b51e4420bd252ddaddfaafa4cdaaa0bb8bdc 6576592 freebayes-dbgsym_1.3.6-2_amd64.deb 9e4572a5f1c574812dea063ba86f68e97dc018bdbc131d0b4ffef5ce19a4bbe1 1469624 freebayes_1.3.6-2_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Tue, 08 Nov 2022 02:50:24 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-9), autotools-dev (= 20220109.1), base-files (= 12.3), base-passwd (= 3.6.1), bash (= 5.2-2+b1), bc (= 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SOURCE_DATE_EPOCH="1667309931" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes-dbgsym_1.3.6-2_amd64.deb ---------------------------------- new Debian package, version 2.0. size 6576592 bytes: control archive=644 bytes. 420 bytes, 12 lines control 298 bytes, 3 lines md5sums Package: freebayes-dbgsym Source: freebayes Version: 1.3.6-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 6655 Depends: freebayes (= 1.3.6-2) Section: debug Priority: optional Description: debug symbols for freebayes Build-Ids: 724276f6c785560032eca58c81b99fed7573a31e eee616468ee6017272fadf93ccb1bcd596dd9421 drwxr-xr-x root/root 0 2022-11-01 13:38 ./ drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/ drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/ drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/ drwxr-xr-x 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bytes. 855 bytes, 17 lines control 5545 bytes, 66 lines md5sums Package: freebayes Version: 1.3.6-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3904 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libseqlib2 (>= 1.2.0), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.3+dfsg), zlib1g (>= 1:1.1.4), python3 Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2022-11-01 13:38 ./ drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/ drwxr-xr-x root/root 0 2022-11-01 13:38 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./usr/share/doc/freebayes/examples/tiny/1read.bam.bai -rw-r--r-- root/root 287213 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam -rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam.bai -rw-r--r-- root/root 155615 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.cram -rw-r--r-- root/root 16307 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.giab.vcf -rw-r--r-- root/root 287228 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam -rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam.bai -rw-r--r-- root/root 12581 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.fa -rw-r--r-- root/root 33 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.fa.fai -rw-r--r-- root/root 2394 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/hla.vcf.gz 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./usr/share/doc/freebayes/examples/tiny/q_spiked.vcf.gz.tbi -rw-r--r-- root/root 924 2022-11-01 13:38 ./usr/share/doc/freebayes/run-unit-test.gz drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/freebayes/ drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/freebayes/scripts/ -rw-r--r-- root/root 1034 2022-01-21 09:38 ./usr/share/freebayes/scripts/GenerateFreebayesRegions.R -rwxr-xr-x root/root 234 2022-01-21 09:38 ./usr/share/freebayes/scripts/bgziptabix -rwxr-xr-x root/root 1495 2022-01-21 09:38 ./usr/share/freebayes/scripts/coverage_to_regions.py -rwxr-xr-x root/root 2574 2022-01-21 09:38 ./usr/share/freebayes/scripts/fasta_generate_regions.py -rwxr-xr-x root/root 1558 2022-01-21 09:38 ./usr/share/freebayes/scripts/freebayes-parallel -rwxr-xr-x root/root 706 2022-01-21 09:38 ./usr/share/freebayes/scripts/generate_freebayes_region_scripts.sh -rw-r--r-- root/root 760 2022-11-01 13:38 ./usr/share/freebayes/scripts/sam_add_rg.pl -rw-r--r-- root/root 371 2022-01-21 09:38 ./usr/share/freebayes/scripts/samples.cnv -rw-r--r-- root/root 6414 2022-01-21 09:38 ./usr/share/freebayes/scripts/split_ref_by_bai_datasize.py -rwxr-xr-x root/root 839 2022-01-21 09:38 ./usr/share/freebayes/scripts/update_version.sh -rwxr-xr-x root/root 315 2022-01-21 09:38 ./usr/share/freebayes/scripts/vcffirstheader lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [645 B] Get:5 copy:/<>/apt_archive ./ Packages [712 B] Fetched 2320 B in 0s (56.0 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After this operation, 51.2 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://mirror.einval.org/debian sid/main arm64 netbase all 6.4 [12.8 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 openssl arm64 3.0.7-1 [1367 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 ca-certificates all 20211016 [156 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-5 [45.9 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.40-1 [556 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.40-1 [903 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 iso-codes all 4.12.0-1 [2888 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40+b2 [66.1 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b1 [10.4 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b4 [15.5 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-2+b1 [22.9 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:20 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.63-1+b1 [42.8 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libberkeleydb-perl arm64 0.64-2+b1 [121 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:26 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.16-1 [90.3 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libhtml-parser-perl arm64 3.79-1+b1 [98.8 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libcgi-pm-perl all 4.54-1 [224 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:30 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-2 [19.4 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b1 [35.3 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.46-1 [13.5 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.28-2 [16.4 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-2+b1 [24.2 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-3 [9724 B] Get:36 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:39 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.32-1+b1 [128 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.004003-1 [39.0 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-3+b1 [37.5 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1+b1 [34.0 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b1 [98.8 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-2+b1 [24.2 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.05-1+b1 [28.3 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libhtml-form-perl all 6.10-1 [24.0 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libhtml-tree-perl all 5.07-2 [213 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get:74 http://mirror.einval.org/debian sid/main arm64 libnet-ssleay-perl arm64 1.92-2+b1 [308 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libio-socket-ssl-perl all 2.075-1 [220 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libwww-perl all 6.67-1 [194 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004004-1 [13.3 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-3 [36.5 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.12-1 [16.1 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 liblz1 arm64 1.13-4 [40.8 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:97 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b3 [167 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-2+b1 [11.1 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-2+b1 [12.4 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.124-1 [56.1 kB] Get:103 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.20-1+b1 [17.1 kB] Get:104 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.010-1 [11.2 kB] Get:105 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1+b2 [42.4 kB] Get:106 http://mirror.einval.org/debian sid/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:107 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 5.001+ds-1+b1 [97.5 kB] Get:108 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 5.001+ds-1+b1 [99.1 kB] Get:109 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-2 [10.7 kB] Get:110 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.26-1 [53.3 kB] Get:111 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.27-1+b1 [28.4 kB] Get:112 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-2+b1 [24.1 kB] Get:113 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b1 [8396 B] Get:114 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1+b2 [12.6 kB] Get:115 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1+b2 [196 kB] Get:116 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:117 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-2+b1 [72.2 kB] Get:118 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b4 [19.7 kB] Get:119 http://mirror.einval.org/debian sid/main arm64 libwww-mechanize-perl all 2.15-1 [120 kB] Get:120 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get:121 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.84+ds-1+b1 [33.1 kB] Get:122 http://mirror.einval.org/debian sid/main arm64 plzip arm64 1.10-4 [60.7 kB] Get:123 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:124 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:125 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:126 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-27 [163 kB] Get:127 http://mirror.einval.org/debian sid/main arm64 lintian all 2.115.3 [1417 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.9 MB in 0s (36.7 MB/s) Selecting previously unselected package netbase. (Reading database ... 21149 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.7-1_arm64.deb ... Unpacking openssl (3.0.7-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) ... Selecting previously unselected package diffstat. Preparing to unpack .../003-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../004-libassuan0_2.5.5-5_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../005-gpgconf_2.2.40-1_arm64.deb ... Unpacking gpgconf (2.2.40-1) ... Selecting previously unselected package gpg. Preparing to unpack .../006-gpg_2.2.40-1_arm64.deb ... 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Preparing to unpack .../126-sbuild-build-depends-lintian-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b2) ... Setting up liblz1:arm64 (1.13-4) ... Setting up libberkeleydb-perl:arm64 (0.64-2+b1) ... Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-1+b4) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.13-2) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.46-1) ... 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Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:arm64 (3.79-1+b1) ... Setting up libio-socket-ssl-perl (2.075-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhtml-form-perl (6.10-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl:arm64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-3) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.15-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up lintian (2.115.3) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.36-4) ... Processing triggers for man-db (2.11.0-1+b1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 103412 Build-Time: 364 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 112 Job: freebayes_1.3.6-2 Lintian: pass Machine Architecture: arm64 Package: freebayes Package-Time: 512 Source-Version: 1.3.6-2 Space: 103412 Status: successful Version: 1.3.6-2 -------------------------------------------------------------------------------- Finished at 2022-11-08T02:50:25Z Build needed 00:08:32, 103412k disk space