sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir +==============================================================================+ | blasr 5.3.5+dfsg-1 (amd64) Mon, 06 Dec 2021 17:52:52 +0000 | +==============================================================================+ Package: blasr Version: 5.3.5+dfsg-1 Source Version: 5.3.5+dfsg-1 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-16b2a7d1-15bc-4205-b1c5-cf8b385c2848' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-PscJiC/resolver-RyrPm5' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [165 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 [8866 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9400 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8731 kB] Fetched 27.2 MB in 7s (3807 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: 'blasr' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/blasr.git Please use: git clone https://salsa.debian.org/med-team/blasr.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 137 kB of source archives. Get:1 http://mirror.einval.org/debian sid/main blasr 5.3.5+dfsg-1 (dsc) [2158 B] Get:2 http://mirror.einval.org/debian sid/main blasr 5.3.5+dfsg-1 (tar) [124 kB] Get:3 http://mirror.einval.org/debian sid/main blasr 5.3.5+dfsg-1 (diff) [10.9 kB] Fetched 137 kB in 1s (248 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/blasr-PscJiC/blasr-5.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-PscJiC' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~), 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), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~), 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 [490 B] Get:5 copy:/<>/apt_archive ./ Packages [581 B] Fetched 2028 B in 0s (47.9 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 binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dpkg-cross dwz emacsen-common file g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base googletest groff-base hdf5-helpers:amd64 intltool-debian libaec-dev:amd64 libaec0:amd64 libarchive-zip-perl libarchive13 libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblasr-dev:amd64 libblasr5.3.5:amd64 libboost-dev:amd64 libboost1.74-dev:amd64 libbrotli1 libbrotli1: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 libcurl4:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1 libexpat1 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libglib2.0-0 libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgtest-dev:amd64 libhdf5-103-1:amd64 libhdf5-cpp-103-1:amd64 libhdf5-dev:amd64 libhdf5-fortran-102:amd64 libhdf5-hl-100:amd64 libhdf5-hl-cpp-100:amd64 libhdf5-hl-fortran-100:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu67 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjpeg-dev:amd64 libjpeg62-turbo:amd64 libjpeg62-turbo-dev:amd64 libjsoncpp24 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.4-2 libldap-2.4-2:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libmpdec3 libncurses6 libncursesw6 libnettle8:amd64 libnghttp2-14 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpbbam-dev:amd64 libpbbam1.6.0:amd64 libpbcopper-dev:amd64 libpbcopper1.8.0:amd64 libpbcopper1.9.3:amd64 libpbdata-dev:amd64 libpbihdf-dev:amd64 libpbseq-dev:amd64 libpipeline1 libprocps8 libpsl5 libpsl5:amd64 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 librhash0 librtmp1 librtmp1:amd64 libsasl2-2 libsasl2-2:amd64 libsasl2-modules-db libsasl2-modules-db:amd64 libsigsegv2 libsqlite3-0 libssh2-1 libssh2-1:amd64 libssl-dev:amd64 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsz2:amd64 libtasn1-6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types meson ninja-build pkg-config po-debconf procps python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal readline-common sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc gcc-11-locales cpp-doc dh-make binutils-multiarch g++-11-multilib-x86-64-linux-gnu gcc-11-doc gcc-11-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc:amd64 libboost1.74-doc:amd64 libboost-atomic1.74-dev:amd64 libboost-chrono1.74-dev:amd64 libboost-container1.74-dev:amd64 libboost-context1.74-dev:amd64 libboost-contract1.74-dev:amd64 libboost-coroutine1.74-dev:amd64 libboost-date-time1.74-dev:amd64 libboost-exception1.74-dev:amd64 libboost-fiber1.74-dev:amd64 libboost-filesystem1.74-dev:amd64 libboost-graph1.74-dev:amd64 libboost-graph-parallel1.74-dev:amd64 libboost-iostreams1.74-dev:amd64 libboost-locale1.74-dev:amd64 libboost-log1.74-dev:amd64 libboost-math1.74-dev:amd64 libboost-mpi1.74-dev:amd64 libboost-mpi-python1.74-dev:amd64 libboost-numpy1.74-dev:amd64 libboost-program-options1.74-dev:amd64 libboost-python1.74-dev:amd64 libboost-random1.74-dev:amd64 libboost-regex1.74-dev:amd64 libboost-serialization1.74-dev:amd64 libboost-stacktrace1.74-dev:amd64 libboost-system1.74-dev:amd64 libboost-test1.74-dev:amd64 libboost-thread1.74-dev:amd64 libboost-timer1.74-dev:amd64 libboost-type-erasure1.74-dev:amd64 libboost-wave1.74-dev:amd64 libboost1.74-tools-dev:amd64 libmpfrc++-dev:amd64 libntl-dev:amd64 libboost-nowide1.74-dev: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 gnutls-bin:amd64 krb5-doc:amd64 krb5-user:amd64 libhdf5-doc:amd64 liblzma-doc:amd64 libssl-doc:amd64 libstdc++-11-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 python3-setuptools python3.9-venv python3.9-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx ca-certificates:amd64 ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales:amd64 libldap-common libldap-common:amd64 libgpm2 publicsuffix publicsuffix:amd64 libsasl2-modules libsasl2-modules:amd64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-11-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dpkg-cross dwz emacsen-common file g++-11-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-11-base:amd64 gcc-11-cross-base gcc-11-x86-64-linux-gnu gcc-11-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base googletest groff-base hdf5-helpers:amd64 intltool-debian libaec-dev:amd64 libaec0:amd64 libarchive-zip-perl libarchive13 libasan6:amd64 libasan6-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblasr-dev:amd64 libblasr5.3.5:amd64 libboost-dev:amd64 libboost1.74-dev:amd64 libbrotli1 libbrotli1: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 libcurl4:amd64 libcurl4-gnutls-dev:amd64 libdb5.3:amd64 libdebhelper-perl libdebian-dpkgcross-perl libdeflate-dev:amd64 libdeflate0:amd64 libelf1 libexpat1 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:amd64 libgcc-11-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libglib2.0-0 libgmp10:amd64 libgnutls30:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libgtest-dev:amd64 libhdf5-103-1:amd64 libhdf5-cpp-103-1:amd64 libhdf5-dev:amd64 libhdf5-fortran-102:amd64 libhdf5-hl-100:amd64 libhdf5-hl-cpp-100:amd64 libhdf5-hl-fortran-100:amd64 libhogweed6:amd64 libhts-dev:amd64 libhts3:amd64 libhtscodecs2:amd64 libicu67 libidn2-0:amd64 libio-string-perl libitm1:amd64 libitm1-amd64-cross libjpeg-dev:amd64 libjpeg62-turbo:amd64 libjpeg62-turbo-dev:amd64 libjsoncpp24 libk5crypto3:amd64 libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64 libldap-2.4-2 libldap-2.4-2:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma-dev:amd64 liblzma5:amd64 libmagic-mgc libmagic1 libmpdec3 libncurses6 libncursesw6 libnettle8:amd64 libnghttp2-14 libnghttp2-14:amd64 libnsl-dev:amd64 libnsl2:amd64 libp11-kit0:amd64 libpbbam-dev:amd64 libpbbam1.6.0:amd64 libpbcopper-dev:amd64 libpbcopper1.8.0:amd64 libpbcopper1.9.3:amd64 libpbdata-dev:amd64 libpbihdf-dev:amd64 libpbseq-dev:amd64 libpipeline1 libprocps8 libpsl5 libpsl5:amd64 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 librhash0 librtmp1 librtmp1:amd64 libsasl2-2 libsasl2-2:amd64 libsasl2-modules-db libsasl2-modules-db:amd64 libsigsegv2 libsqlite3-0 libssh2-1 libssh2-1:amd64 libssl-dev:amd64 libssl1.1:amd64 libstdc++-11-dev:amd64 libstdc++-11-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsz2:amd64 libtasn1-6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring2:amd64 libuv1 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types meson ninja-build pkg-config po-debconf procps python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3.9 python3.9-minimal readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils ucf zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 204 newly installed, 0 to remove and 0 not upgraded. Need to get 268 MB of archives. After this operation, 1091 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1008 B] Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-4 [143 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-7 [883 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.4-1 [34.6 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.9-1 [800 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.1-3 [89.8 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.9-1 [1839 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.9.8-1 [38.5 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arm64 autoconf all 2.71-2 [343 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.1 [823 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-5+b1 [633 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b3 [270 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg2-2 [74.3 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libsasl2-2 arm64 2.1.27+dfsg2-2 [110 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libldap-2.4-2 arm64 2.4.59+dfsg-1 [222 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libssh2-1 arm64 1.10.0-2 [172 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libcurl4 arm64 7.79.1-2 [338 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libjsoncpp24 arm64 1.9.4-5 [72.5 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 librhash0 arm64 1.4.2-1 [127 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libuv1 arm64 1.42.0-1 [129 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 dh-elpa-helper all 2.0.9 [11.2 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 emacsen-common all 3.0.4 [19.3 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 cmake-data all 3.22.0-1 [1902 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 cmake arm64 3.22.0-1 [5431 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu-base arm64 11.2.0-9cross1 [205 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 cpp-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [48.2 MB] Get:59 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:11.2.0-2 [17.0 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.37-10 [2303 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-9cross1 [201 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-amd64-cross all 11.2.0-9cross1 [42.0 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libgomp1-amd64-cross all 11.2.0-9cross1 [104 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 11.2.0-9cross1 [25.5 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 11.2.0-9cross1 [8764 B] Get:67 http://mirror.einval.org/debian sid/main arm64 libasan6-amd64-cross all 11.2.0-9cross1 [2044 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 liblsan0-amd64-cross all 11.2.0-9cross1 [885 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libtsan0-amd64-cross all 11.2.0-9cross1 [2010 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.32-1cross4 [1570 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libstdc++6-amd64-cross all 11.2.0-9cross1 [535 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libubsan1-amd64-cross all 11.2.0-9cross1 [834 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libquadmath0-amd64-cross all 11.2.0-9cross1 [145 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libgcc-11-dev-amd64-cross all 11.2.0-9cross1 [2357 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 gcc-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [54.7 MB] Get:76 http://mirror.einval.org/debian sid/main arm64 gcc-x86-64-linux-gnu arm64 4:11.2.0-2 [1460 B] Get:77 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 5.10.46-4cross4 [1468 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.32-1cross4 [2248 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libstdc++-11-dev-amd64-cross all 11.2.0-9cross1 [1952 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 g++-11-x86-64-linux-gnu arm64 11.2.0-9cross1 [52.2 MB] Get:81 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:11.2.0-2 [1176 B] Get:82 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:96 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.5.2 [192 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.1-1 [15.6 kB] Get:103 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.186-1 [177 kB] Get:104 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:105 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB] Get:106 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:107 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:108 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.5.2 [1056 kB] Get:109 http://mirror.einval.org/debian sid/main arm64 googletest all 1.11.0-3 [535 kB] Get:110 http://mirror.einval.org/debian sid/main amd64 hdf5-helpers amd64 1.10.7+repack-4 [42.8 kB] Get:111 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 11.2.0-12 [42.0 kB] Get:112 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.32-5 [2820 kB] Get:113 http://mirror.einval.org/debian sid/main amd64 libaec0 amd64 1.0.6-1 [20.3 kB] Get:114 http://mirror.einval.org/debian sid/main amd64 libsz2 amd64 1.0.6-1 [7492 B] Get:115 http://mirror.einval.org/debian sid/main amd64 libaec-dev amd64 1.0.6-1 [18.9 kB] Get:116 http://mirror.einval.org/debian sid/main amd64 libasan6 amd64 11.2.0-12 [2049 kB] Get:117 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 11.2.0-12 [9064 B] Get:118 http://mirror.einval.org/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b3 [276 kB] Get:119 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.4-1 [75.2 kB] Get:120 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.18.3-7 [65.4 kB] Get:121 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.18.3-7 [113 kB] Get:122 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:123 http://mirror.einval.org/debian sid/main amd64 libssl1.1 amd64 1.1.1l-1 [1555 kB] Get:124 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.18.3-7 [363 kB] Get:125 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.18.3-7 [165 kB] Get:126 http://mirror.einval.org/debian sid/main amd64 libunistring2 amd64 0.9.10-6 [384 kB] Get:127 http://mirror.einval.org/debian sid/main amd64 libidn2-0 amd64 2.3.2-2 [95.3 kB] Get:128 http://mirror.einval.org/debian sid/main amd64 libgmp10 amd64 2:6.2.1+dfsg-3 [560 kB] Get:129 http://mirror.einval.org/debian sid/main amd64 libnettle8 amd64 3.7.3-1 [270 kB] Get:130 http://mirror.einval.org/debian sid/main amd64 libhogweed6 amd64 3.7.3-1 [320 kB] Get:131 http://mirror.einval.org/debian sid/main amd64 libffi8 amd64 3.4.2-3 [24.8 kB] Get:132 http://mirror.einval.org/debian sid/main amd64 libp11-kit0 amd64 0.24.0-6 [347 kB] Get:133 http://mirror.einval.org/debian sid/main amd64 libtasn1-6 amd64 4.18.0-4 [55.9 kB] Get:134 http://mirror.einval.org/debian sid/main amd64 libgnutls30 amd64 3.7.2-2 [1350 kB] Get:135 http://mirror.einval.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.8 [687 kB] Get:136 http://mirror.einval.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-2 [74.1 kB] Get:137 http://mirror.einval.org/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg2-2 [110 kB] Get:138 http://mirror.einval.org/debian sid/main amd64 libldap-2.4-2 amd64 2.4.59+dfsg-1 [232 kB] Get:139 http://mirror.einval.org/debian sid/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:140 http://mirror.einval.org/debian sid/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:141 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] Get:142 http://mirror.einval.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:143 http://mirror.einval.org/debian sid/main amd64 libssh2-1 amd64 1.10.0-2 [178 kB] Get:144 http://mirror.einval.org/debian sid/main amd64 libcurl4 amd64 7.79.1-2 [360 kB] Get:145 http://mirror.einval.org/debian sid/main amd64 libhdf5-103-1 amd64 1.10.7+repack-4 [1236 kB] Get:146 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-12 [576 kB] Get:147 http://mirror.einval.org/debian sid/main amd64 libhdf5-cpp-103-1 amd64 1.10.7+repack-4 [145 kB] Get:148 http://mirror.einval.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5 [46.2 kB] Get:149 http://mirror.einval.org/debian sid/main amd64 libcurl3-gnutls amd64 7.79.1-2 [355 kB] Get:150 http://mirror.einval.org/debian sid/main amd64 libdeflate0 amd64 1.8-1 [53.1 kB] Get:151 http://mirror.einval.org/debian sid/main amd64 libhtscodecs2 amd64 1.1.1-3+b1 [50.1 kB] Get:152 http://mirror.einval.org/debian sid/main amd64 liblzma5 amd64 5.2.5-2 [168 kB] Get:153 http://mirror.einval.org/debian sid/main amd64 libhts3 amd64 1.13+ds-2 [395 kB] Get:154 http://mirror.einval.org/debian sid/main amd64 libpbcopper1.8.0 amd64 1.8.0+dfsg-2+b1 [452 kB] Get:155 http://mirror.einval.org/debian sid/main amd64 libpbbam1.6.0 amd64 1.6.0+dfsg-2 [687 kB] Get:156 http://mirror.einval.org/debian sid/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-2 [1099 kB] Get:157 http://mirror.einval.org/debian sid/main amd64 libpbcopper1.9.3 amd64 1.9.3+dfsg-2 [595 kB] Get:158 http://mirror.einval.org/debian sid/main amd64 libpbcopper-dev amd64 1.9.3+dfsg-2 [886 kB] Get:159 http://mirror.einval.org/debian sid/main amd64 libpbdata-dev amd64 5.3.5+dfsg-2 [41.1 kB] Get:160 http://mirror.einval.org/debian sid/main amd64 libblasr-dev amd64 5.3.5+dfsg-2 [2070 kB] Get:161 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 11.2.0-12 [106 kB] Get:162 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 11.2.0-12 [26.1 kB] Get:163 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 11.2.0-12 [886 kB] Get:164 http://mirror.einval.org/debian sid/main amd64 libtsan0 amd64 11.2.0-12 [2018 kB] Get:165 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 11.2.0-12 [835 kB] Get:166 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 11.2.0-12 [145 kB] Get:167 http://mirror.einval.org/debian sid/main amd64 libgcc-11-dev amd64 11.2.0-12 [2359 kB] Get:168 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 5.15.5-1 [1457 kB] Get:169 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.26-1 [88.9 kB] Get:170 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.26-1 [104 kB] Get:171 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB] Get:172 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:173 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB] Get:174 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:175 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.32-5 [2251 kB] Get:176 http://mirror.einval.org/debian sid/main amd64 libstdc++-11-dev amd64 11.2.0-12 [1973 kB] Get:177 http://mirror.einval.org/debian sid/main amd64 libboost1.74-dev amd64 1.74.0-13 [9537 kB] Get:178 http://mirror.einval.org/debian sid/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:179 http://mirror.einval.org/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.79.1-2 [446 kB] Get:180 http://mirror.einval.org/debian sid/main amd64 libdeflate-dev amd64 1.8-1 [46.7 kB] Get:181 http://mirror.einval.org/debian sid/main amd64 libgfortran5 amd64 11.2.0-12 [709 kB] Get:182 http://mirror.einval.org/debian sid/main arm64 libglib2.0-0 arm64 2.70.2-1 [1313 kB] Get:183 http://mirror.einval.org/debian sid/main amd64 libgtest-dev amd64 1.11.0-3 [234 kB] Get:184 http://mirror.einval.org/debian sid/main amd64 libhdf5-fortran-102 amd64 1.10.7+repack-4 [108 kB] Get:185 http://mirror.einval.org/debian sid/main amd64 libhdf5-hl-100 amd64 1.10.7+repack-4 [84.1 kB] Get:186 http://mirror.einval.org/debian sid/main amd64 libhdf5-hl-fortran-100 amd64 1.10.7+repack-4 [59.2 kB] Get:187 http://mirror.einval.org/debian sid/main amd64 libhdf5-hl-cpp-100 amd64 1.10.7+repack-4 [40.2 kB] Get:188 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:189 http://mirror.einval.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.2-1 [164 kB] Get:190 http://mirror.einval.org/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:2.1.2-1 [288 kB] Get:191 http://mirror.einval.org/debian sid/main amd64 libjpeg-dev amd64 1:2.1.2-1 [74.7 kB] Get:192 http://mirror.einval.org/debian sid/main amd64 libssl-dev amd64 1.1.1l-1 [1809 kB] Get:193 http://mirror.einval.org/debian sid/main amd64 libhdf5-dev amd64 1.10.7+repack-4 [2495 kB] Get:194 http://mirror.einval.org/debian sid/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get:195 http://mirror.einval.org/debian sid/main amd64 libhts-dev amd64 1.13+ds-2 [4086 kB] Get:196 http://mirror.einval.org/debian sid/main amd64 libpbbam-dev amd64 1.6.0+dfsg-2 [87.2 kB] Get:197 http://mirror.einval.org/debian sid/main amd64 libpbihdf-dev amd64 5.3.5+dfsg-2 [47.6 kB] Get:198 http://mirror.einval.org/debian sid/main amd64 libpbseq-dev amd64 5.3.5+dfsg-2 [5356 B] Get:199 http://mirror.einval.org/debian sid/main arm64 ninja-build arm64 1.10.1-1 [107 kB] Get:200 http://mirror.einval.org/debian sid/main arm64 python3-pkg-resources all 59.4.0-1 [196 kB] Get:201 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.9.9-2 [79.5 kB] Get:202 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.9.9-2 [146 kB] Get:203 http://mirror.einval.org/debian sid/main arm64 meson all 0.60.2-1 [512 kB] Get:204 http://mirror.einval.org/debian sid/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 268 MB in 8s (35.3 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12340 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.37.2-4_arm64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-7_arm64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.4-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../6-libpython3.9-minimal_3.9.9-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../7-libexpat1_2.4.1-3_arm64.deb ... Unpacking libexpat1:arm64 (2.4.1-3) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../8-python3.9-minimal_3.9.9-1_arm64.deb ... Unpacking python3.9-minimal (3.9.9-1) ... Setting up libpython3.9-minimal:arm64 (3.9.9-1) ... Setting up libexpat1:arm64 (2.4.1-3) ... Setting up python3.9-minimal (3.9.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13222 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.8-1_arm64.deb ... Unpacking python3-minimal (3.9.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... 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_6.3-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.3-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.1-2_all.deb ... Unpacking readline-common (8.1-2) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../5-libreadline8_8.1-2_arm64.deb ... Unpacking libreadline8:arm64 (8.1-2) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../6-libsqlite3-0_3.36.0-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.36.0-2) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.9-1_arm64.deb ... 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Setting up libfile-stripnondeterminism-perl (1.12.1-1) ... Setting up gettext (0.21-4) ... Setting up libgtest-dev:amd64 (1.11.0-3) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2+b1) ... Setting up liblsan0-amd64-cross (11.2.0-9cross1) ... Setting up libc6-dev-amd64-cross (2.32-1cross4) ... Setting up libreadline8:arm64 (8.1-2) ... Setting up libtsan0-amd64-cross (11.2.0-9cross1) ... Setting up libldap-2.4-2:arm64 (2.4.59+dfsg-1) ... Setting up cpp-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up m4 (1.4.18-5) ... Setting up libgomp1-amd64-cross (11.2.0-9cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libitm1-amd64-cross (11.2.0-9cross1) ... Setting up libatomic1-amd64-cross (11.2.0-9cross1) ... Setting up libquadmath0-amd64-cross (11.2.0-9cross1) ... Setting up libubsan1-amd64-cross (11.2.0-9cross1) ... Setting up ucf (3.0043) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.1-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:arm64 (7.79.1-2) ... Setting up libpython3.9-stdlib:arm64 (3.9.9-1) ... Setting up libpython3-stdlib:arm64 (3.9.8-1) ... Setting up cpp-x86-64-linux-gnu (4:11.2.0-2) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgcc-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... 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 dh-autoreconf (20) ... Setting up gcc-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-2+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 libstdc++-11-dev-amd64-cross (11.2.0-9cross1) ... Setting up cmake (3.22.0-1) ... Setting up python3.9 (3.9.9-1) ... Setting up g++-11-x86-64-linux-gnu (11.2.0-9cross1) ... Setting up gcc-x86-64-linux-gnu (4:11.2.0-2) ... Setting up debhelper (13.5.2) ... Setting up python3 (3.9.8-1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-x86-64-linux-gnu (4:11.2.0-2) ... Setting up python3-lib2to3 (3.9.9-2) ... Setting up python3-pkg-resources (59.4.0-1) ... Setting up python3-distutils (3.9.9-2) ... Setting up meson (0.60.2-1) ... Setting up libconfig-auto-perl (0.44-1.1) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-amd64 (12.9) ... Setting up libgcc-s1:amd64 (11.2.0-12) ... Setting up libc6:amd64 (2.32-5) ... Setting up libffi8:amd64 (3.4.2-3) ... Setting up libtasn1-6:amd64 (4.18.0-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5) ... Setting up libdb5.3:amd64 (5.3.28+dfsg1-0.8) ... Setting up libstdc++6:amd64 (11.2.0-12) ... Setting up liblsan0:amd64 (11.2.0-12) ... Setting up libitm1:amd64 (11.2.0-12) ... Setting up libtsan0:amd64 (11.2.0-12) ... Setting up libhtscodecs2:amd64 (1.1.1-3+b1) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up liblzma5:amd64 (5.2.5-2) ... Setting up libssl1.1:amd64 (1.1.1l-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b3) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libunistring2:amd64 (0.9.10-6) ... Setting up libdeflate0:amd64 (1.8-1) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Setting up libcrypt1:amd64 (1:4.4.26-1) ... Setting up libidn2-0:amd64 (2.3.2-2) ... Setting up libcom-err2:amd64 (1.46.4-1) ... Setting up libgomp1:amd64 (11.2.0-12) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up libasan6:amd64 (11.2.0-12) ... Setting up libkrb5support0:amd64 (1.18.3-7) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg2-2) ... Setting up libjpeg62-turbo:amd64 (1:2.1.2-1) ... Setting up libnettle8:amd64 (3.7.3-1) ... Setting up libgmp10:amd64 (2:6.2.1+dfsg-3) ... Setting up libquadmath0:amd64 (11.2.0-12) ... Setting up libp11-kit0:amd64 (0.24.0-6) ... Setting up libssl-dev:amd64 (1.1.1l-1) ... Setting up libatomic1:amd64 (11.2.0-12) ... Setting up libk5crypto3:amd64 (1.18.3-7) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg2-2) ... Setting up libgfortran5:amd64 (11.2.0-12) ... Setting up liblzma-dev:amd64 (5.2.5-2) ... Setting up libubsan1:amd64 (11.2.0-12) ... Setting up libgcc-11-dev:amd64 (11.2.0-12) ... Setting up libcrypt-dev:amd64 (1:4.4.26-1) ... Setting up libpbcopper1.8.0:amd64 (1.8.0+dfsg-2+b1) ... Setting up libssh2-1:amd64 (1.10.0-2) ... Setting up libkrb5-3:amd64 (1.18.3-7) ... Setting up libpbcopper1.9.3:amd64 (1.9.3+dfsg-2) ... Setting up libdeflate-dev:amd64 (1.8-1) ... Setting up libsz2:amd64 (1.0.6-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libhogweed6:amd64 (3.7.3-1) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libgnutls30:amd64 (3.7.2-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-7) ... Setting up libpbcopper-dev:amd64 (1.9.3+dfsg-2) ... Setting up libtirpc3:amd64 (1.3.2-2) ... Setting up libpbdata-dev:amd64 (5.3.5+dfsg-2) ... Setting up libldap-2.4-2:amd64 (2.4.59+dfsg-1) ... Setting up libcurl3-gnutls:amd64 (7.79.1-2) ... Setting up libcurl4-gnutls-dev:amd64 (7.79.1-2) ... Setting up libtirpc-dev:amd64 (1.3.2-2) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libcurl4:amd64 (7.79.1-2) ... Setting up libhts3:amd64 (1.13+ds-2) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4) ... Setting up libc6-dev:amd64 (2.32-5) ... Setting up libpbbam1.6.0:amd64 (1.6.0+dfsg-2) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4) ... Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-2) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.7+repack-4) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.2-1) ... Setting up libblasr-dev:amd64 (5.3.5+dfsg-2) ... Setting up libhdf5-fortran-102:amd64 (1.10.7+repack-4) ... Setting up libstdc++-11-dev:amd64 (11.2.0-12) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.7+repack-4) ... Setting up libboost1.74-dev:amd64 (1.74.0-13) ... Setting up libjpeg-dev:amd64 (1:2.1.2-1) ... Setting up libhts-dev:amd64 (1.13+ds-2) ... Setting up libhdf5-dev:amd64 (1.10.7+repack-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libpbbam-dev:amd64 (1.6.0+dfsg-2) ... Setting up libpbihdf-dev:amd64 (5.3.5+dfsg-2) ... Setting up libpbseq-dev:amd64 (5.3.5+dfsg-2) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.32-5) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.37-10 dpkg-dev_1.21.0 g++-11_11.2.0-12 gcc-11_11.2.0-12 libc6-dev_2.32-5 libstdc++-11-dev_11.2.0-12 libstdc++-11-dev-amd64-cross_11.2.0-9cross1 libstdc++6_11.2.0-12 libstdc++6-amd64-cross_11.2.0-9cross1 linux-libc-dev_5.15.5-1 Package versions: adduser_3.118 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-5 binutils_2.37-10 binutils-aarch64-linux-gnu_2.37-10 binutils-common_2.37-10 binutils-x86-64-linux-gnu_2.37-10 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-5 cmake_3.22.0-1 cmake-data_3.22.0-1 coreutils_8.32-4.1 cpp_4:11.2.0-2 cpp-11_11.2.0-12 cpp-11-x86-64-linux-gnu_11.2.0-9cross1 cpp-x86-64-linux-gnu_4:11.2.0-2 cross-config_2.6.18+nmu2 crossbuild-essential-amd64_12.9 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-elpa-helper_2.0.9 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dpkg_1.21.0 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.21.0 dwz_0.14-1 emacsen-common_3.0.4 fakeroot_1.26-1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-12 g++-11-x86-64-linux-gnu_11.2.0-9cross1 g++-x86-64-linux-gnu_4:11.2.0-2 gcc_4:11.2.0-2 gcc-10-base_10.3.0-13 gcc-11_11.2.0-12 gcc-11-base_11.2.0-12 gcc-11-cross-base_11.2.0-9cross1 gcc-11-x86-64-linux-gnu_11.2.0-9cross1 gcc-11-x86-64-linux-gnu-base_11.2.0-9cross1 gcc-x86-64-linux-gnu_4:11.2.0-2 gettext_0.21-4 gettext-base_0.21-4 googletest_1.11.0-3 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hdf5-helpers_1.10.7+repack-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.3.13 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2+b1 libasan6_11.2.0-12 libasan6-amd64-cross_11.2.0-9cross1 libatomic1_11.2.0-12 libatomic1-amd64-cross_11.2.0-9cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1+b1 libbinutils_2.37-10 libblasr-dev_5.3.5+dfsg-2 libblasr5.3.5_5.3.5+dfsg-2 libblkid1_2.37.2-4 libboost-dev_1.74.0.3 libboost1.74-dev_1.74.0-13 libbrotli1_1.0.9-2+b3 libbz2-1.0_1.0.8-5 libc-bin_2.32-5 libc-dev-bin_2.32-5 libc6_2.32-5 libc6-amd64-cross_2.32-1cross4 libc6-dev_2.32-5 libc6-dev-amd64-cross_2.32-1cross4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-12 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-10 libctf0_2.37-10 libcurl3-gnutls_7.79.1-2 libcurl4_7.79.1-2 libcurl4-gnutls-dev_7.79.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdebian-dpkgcross-perl_2.6.18+nmu2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.21.0 libelf1_0.186-1 libexpat1_2.4.1-3 libfakeroot_1.26-1 libffi8_3.4.2-3 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.1-1 libfile-which-perl_1.23-1 libgcc-11-dev_11.2.0-12 libgcc-11-dev-amd64-cross_11.2.0-9cross1 libgcc-s1_11.2.0-12 libgcc-s1-amd64-cross_11.2.0-9cross1 libgcrypt20_1.9.4-4 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran5_11.2.0-12 libglib2.0-0_2.70.2-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-12 libgomp1-amd64-cross_11.2.0-9cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libgtest-dev_1.11.0-3 libhdf5-103-1_1.10.7+repack-4 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libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpbbam-dev_1.6.0+dfsg-2 libpbbam1.6.0_1.6.0+dfsg-2 libpbcopper-dev_1.9.3+dfsg-2 libpbcopper1.8.0_1.8.0+dfsg-2+b1 libpbcopper1.9.3_1.9.3+dfsg-2 libpbdata-dev_5.3.5+dfsg-2 libpbihdf-dev_5.3.5+dfsg-2 libpbseq-dev_5.3.5+dfsg-2 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.8-1 libpython3.9-minimal_3.9.9-1 libpython3.9-stdlib_3.9.9-1 libquadmath0_11.2.0-12 libquadmath0-amd64-cross_11.2.0-9cross1 libreadline8_8.1-2 librhash0_1.4.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libssh2-1_1.10.0-2 libssl-dev_1.1.1l-1 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ncurses-base_6.3-1 ncurses-bin_6.3-1 ninja-build_1.10.1-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.8-1 python3-distutils_3.9.9-2 python3-lib2to3_3.9.9-2 python3-minimal_3.9.8-1 python3-pkg-resources_59.4.0-1 python3.9_3.9.9-1 python3.9-minimal_3.9.9-1 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: blasr Binary: blasr Architecture: any Version: 5.3.5+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-3~) Package-List: blasr deb science optional arch=any Checksums-Sha1: 334132438305cfaf3d7ee6208bcb4cc4b493be5d 124460 blasr_5.3.5+dfsg.orig.tar.xz 44b31951867314ad6bbb532eba4be819073d8b80 10856 blasr_5.3.5+dfsg-1.debian.tar.xz Checksums-Sha256: 765ac47ae74f56e3bee17e2a3c81d404faf7419e42eb45bc9f2a71c7a5942205 124460 blasr_5.3.5+dfsg.orig.tar.xz 2ed7a287697a329594fc5221f369060abce815c635acd314d5b04b10d64281b3 10856 blasr_5.3.5+dfsg-1.debian.tar.xz Files: 46c888e8f9c606d840b0d9dcc8036b21 124460 blasr_5.3.5+dfsg.orig.tar.xz 32ae8a000fb461b9c53123aaa02bf325 10856 blasr_5.3.5+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFj9J0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFcpw/+OOh8eiMIQRckIn7ooZ2uu1nAh1h+7Fb5 Ni21aVdWM4kF45WPge+kMBs7FjBzCZWzng+YunSPtiMrF7fRoiCrWH7SPysRZBqH o+0fgS4jyN6UPvQQYRSyyEXdVxUee3XCsjPas7w9pob1wr5ykdCYBYRXLzDzgxX+ zW81vdsEgVIlB4/9D02KeefD8zeUHo+WqPO/PRr50Cwx2lhmW2vCIkai+lStj8yF PXWmsDNEE+GLdX7yrH4OMLHzkzTglefDFuLvMbenBEQOsAux3/ojpSeV+bIB3Xmo o4HrnCGXZFvJTW6LZyS1PwhULPCNCF3mU40+2ydVgI4b0tePkpy23jpJyilJzCuP 4wXtyqnrOiq2DO6R6VNDaq8zSYrtq8Tg/slVNzNkKlRh6mXvv3ArNPjZLScOpbxm KlW/xDL8WF4gxLVi4o3VyRhzGQsxHWOFpBN9JDN/axeuqt3EdrP04O1VdQDbGKMu T7VHyf/GIYQOyyV2ZZbVMpdLF5J9S24JFgJ0BCljKwyEOl34uSjtJoKsGqxjvexE wE8kq0bKMigbGTmou6yh0FipZnCrsdUoatK6acFoMpLf9MUyXW4gx5YUQntobiZL TmWo3Q9Wn2/5rw2TEPiP5nxKoU+bqGSZ9ov2NbguGcz4EZ8l10ptFD6hNTWHc44z K4I5tGkhSX0= =bCo1 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.FzIUTfvN/trustedkeys.kbx': General error gpgv: Signature made Mon Oct 11 08:23:57 2021 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 ./blasr_5.3.5+dfsg-1.dsc dpkg-source: info: extracting blasr in /<> dpkg-source: info: unpacking blasr_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch dpkg-source: info: applying 2to3.patch 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-16b2a7d1-15bc-4205-b1c5-cf8b385c2848 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 blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary-arch dh binary-arch --buildsystem=meson dh_update_autotools_config -a -O--buildsystem=meson dh_autoreconf -a -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false cd obj-x86_64-linux-gnu && 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 /<>/blasr-5.3.5\+dfsg/debian/.debhelper/generated/_source/meson-cross-file.conf -Dtests=false 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: 0.60.2 Source dir: /<> Build dir: /<>/obj-x86_64-linux-gnu Build type: cross build Project name: blasr Project version: 5.3.5 C++ compiler for the host machine: /usr/bin/x86_64-linux-gnu-g++ (gcc 11.2.0 "x86_64-linux-gnu-g++ (Debian 11.2.0-9) 11.2.0") C++ linker for the host machine: /usr/bin/x86_64-linux-gnu-g++ ld.bfd 2.37 C++ compiler for the build machine: c++ (gcc 11.2.0 "c++ (Debian 11.2.0-12) 11.2.0") C++ linker for the build machine: c++ ld.bfd 2.37 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 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/x86_64-linux-gnu-pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.5 Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.13+ds Library pbcopper found: YES Configuring BlasrVersion.h using configuration Program /usr/bin/meson found: YES (/usr/bin/meson) Build targets in project: 5 blasr 5.3.5 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 tests : false Found ninja-1.10.1 at /usr/bin/ninja make[1]: Leaving directory '/<>' dh_auto_build -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j1 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<> @BLASR_GIT_SHA1@ '(.*)' /<>/git describe --always '--dirty=*' [2/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 192 | charCount[0]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here 193 | case 0: //A | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 194 | charCount[1]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here 195 | case 1: //C | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 196 | charCount[2]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here 197 | case 2: //G | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 198 | charCount[3]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here 199 | case 3: //T | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 200 | charCount[4]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ [3/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp [4/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../extrautils/SWMatcher.cpp:2: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [5/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp [6/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp [7/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/vector:64, from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [8/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp [9/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp [10/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [11/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp [12/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp [13/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../utils/SamToM4.cpp:19: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [14/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../utils/SamToCmpH5.cpp:1: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp: In instantiation of ‘unsigned int AlignmentSetToCmpH5Adapter::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile >; std::string = std::__cxx11::basic_string]’: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:32: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidateList(std::vector >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ ../utils/SamToCmpH5.cpp:199:56: required from here /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:45: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); In file included from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ [15/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../utils/SDPMatcher.cpp:3: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [16/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_LoadPulses.cpp.o -MF libblasr_impl.a.p/utils_LoadPulses.cpp.o.d -o libblasr_impl.a.p/utils_LoadPulses.cpp.o -c ../utils/LoadPulses.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/bits/stl_tree.h:64, from /usr/x86_64-linux-gnu/include/c++/11/map:60, from ../utils/LoadPulses.cpp:6: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [17/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp [18/25] /usr/bin/x86_64-linux-gnu-g++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../utils/SamFilter.cpp:29: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [19/25] rm -f libblasr_impl.a && /usr/bin/x86_64-linux-gnu-ar csrD libblasr_impl.a libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o libblasr_impl.a.p/extrautils_SAModify.cpp.o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o libblasr_impl.a.p/extrautils_SALS.cpp.o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o libblasr_impl.a.p/extrautils_Evolve.cpp.o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o libblasr_impl.a.p/utils_SamToM4.cpp.o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o libblasr_impl.a.p/utils_SDPMatcher.cpp.o libblasr_impl.a.p/utils_LoadPulses.cpp.o libblasr_impl.a.p/utils_PulseToFasta.cpp.o libblasr_impl.a.p/utils_SamFilter.cpp.o [20/25] /usr/bin/x86_64-linux-gnu-g++ -Iblasr.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ blasr.p/Blasr.cpp.o -MF blasr.p/Blasr.cpp.o.d -o blasr.p/Blasr.cpp.o -c ../Blasr.cpp In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5, from ../Blasr.cpp:3: ../iblasr/BlasrMiscsImpl.hpp: In function ‘void MakeSubreadIntervals(std::vector&, std::vector&)’: ../iblasr/BlasrMiscsImpl.hpp:136:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 136 | for (auto subread : subreads) { | ^~~~~~~~ In file included from /usr/include/pbseq/pbdata/CCSSequence.hpp:5, from /usr/include/pbseq/alignment/files/CCSIterator.hpp:4, from ../iblasr/BlasrHeaders.h:57, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from ../iblasr/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: ../iblasr/MappingParameters.h: In copy constructor ‘MappingParameters::MappingParameters(const MappingParameters&)’: ../iblasr/MappingParameters.h:19:7: warning: implicitly-declared ‘constexpr AnchorParameters::AnchorParameters(const AnchorParameters&)’ is deprecated [-Wdeprecated-copy] 19 | class MappingParameters | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:7, from ../iblasr/BlasrHeaders.h:42, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/anchoring/AnchorParameters.hpp:33:23: note: because ‘AnchorParameters’ has user-provided ‘AnchorParameters& AnchorParameters::operator=(const AnchorParameters&)’ 33 | AnchorParameters &operator=(const AnchorParameters &rhs); | ^~~~~~~~ ../Blasr.cpp: In function ‘void MapReadsNonCCS(MappingData >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector&, MappingParameters&, const int&, ReadAlignments&, std::ofstream&)’: ../Blasr.cpp:382:49: note: synthesized method ‘MappingParameters::MappingParameters(const MappingParameters&)’ first required here 382 | MappingParameters sensitiveParams = params; | ^~~~~~ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1407:32: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] 1407 | (void *(*)(void *))MapReads, &mapdb[procIndex]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:951:38: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 27 | if (dynamic_cast(&read) == NULL) { | ^ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/x86_64-linux-gnu/include/c++/11/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ /usr/x86_64-linux-gnu/include/c++/11/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/11/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/11/string:41, from /usr/x86_64-linux-gnu/include/c++/11/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/11/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/11/ios:42, from /usr/x86_64-linux-gnu/include/c++/11/ostream:38, from /usr/x86_64-linux-gnu/include/c++/11/iostream:39, from ../iblasr/BlasrHeaders.h:10, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/x86_64-linux-gnu/include/c++/11/ext/new_allocator.h:162:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 162 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:512:23: required from ‘int GuidedAlign(QSequence&, TSequence&, T_ScoreFn&, int, int, int, float, T_BufferCache&, blasr::Alignment&, AlignmentType, bool, int) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrAlignImpl.hpp:1449:20: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrUtilsImpl.hpp:639:19: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:689:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:698:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] In file included from /usr/x86_64-linux-gnu/include/c++/11/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp: In instantiation of ‘int OneGapAlign(T_QuerySequence&, T_RefSequence&, T_ScoreFunction&, T_BufferList&, blasr::Alignment&) [with T_QuerySequence = FASTQSequence; T_RefSequence = DNASequence; T_ScoreFunction = DistanceMatrixScoreFunction; T_BufferList = MappingBuffers]’: ../iblasr/BlasrAlignImpl.hpp:918:40: required from ‘void AlignIntervals(T_TargetSequence&, T_QuerySequence&, T_QuerySequence&, WeightedIntervalSet&, int (*)[5], int, int, int, int, SequenceIndexDatabase&, std::vector*>&, MappingParameters&, MappingBuffers&, int) [with T_TargetSequence = FASTASequence; T_QuerySequence = SMRTSequence; TDBSequence = FASTQSequence]’ ../iblasr/BlasrAlignImpl.hpp:280:23: required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr&, T_TupleCountTable&, SequenceIndexDatabase&, MappingParameters&, MappingMetrics&, std::vector*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray >; T_TupleCountTable = TupleCountTable; BWT = Bwt; MappingIPC = MappingData >, FASTASequence, DNATuple>]’ ../Blasr.cpp:347:16: required from here /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp:337:40: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 337 | assert(distanceBetweenLeftAndRight >= 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1301:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1310:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 27 | if (dynamic_cast(&read) == NULL) { | ^~ [21/25] /usr/bin/x86_64-linux-gnu-g++ -o blasr blasr.p/Blasr.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/lib/gcc-cross/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/x86_64-linux-gnu/libpbbam.so, may conflict with libpbcopper.so.1.9.3 [22/25] /usr/bin/x86_64-linux-gnu-g++ -Isawriter.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ sawriter.p/utils_SAWriter.cpp.o -MF sawriter.p/utils_SAWriter.cpp.o.d -o sawriter.p/utils_SAWriter.cpp.o -c ../utils/SAWriter.cpp [23/25] /usr/bin/x86_64-linux-gnu-g++ -o sawriter sawriter.p/utils_SAWriter.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/lib/gcc-cross/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/x86_64-linux-gnu/libblasr.so, may conflict with libpbcopper.so.1.9.3 [24/25] /usr/bin/x86_64-linux-gnu-g++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++17 -isystem /usr/include/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp [25/25] /usr/bin/x86_64-linux-gnu-g++ -o toAfg toAfg.p/utils_ToAfg.cpp.o -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-z,relro libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group /usr/lib/gcc-cross/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/bin/ld: warning: libpbcopper.so.1.8.0, needed by /usr/lib/x86_64-linux-gnu/libpbbam.so, may conflict with libpbcopper.so.1.9.3 dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=meson" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson dh_prep -a -O--buildsystem=meson dh_auto_install --destdir=debian/blasr/ -a -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/<>/blasr-5.3.5\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command [1/2] Installing files. Installing blasr to /<>/debian/blasr/usr/bin Installing sawriter to /<>/debian/blasr/usr/bin dh_install -a -O--buildsystem=meson dh_installdocs -a -O--buildsystem=meson dh_installchangelogs -a -O--buildsystem=meson dh_installexamples -a -O--buildsystem=meson dh_installman -a -O--buildsystem=meson dh_installsystemduser -a -O--buildsystem=meson dh_lintian -a -O--buildsystem=meson dh_perl -a -O--buildsystem=meson dh_link -a -O--buildsystem=meson dh_strip_nondeterminism -a -O--buildsystem=meson dh_compress -a -O--buildsystem=meson dh_fixperms -a -O--buildsystem=meson dh_missing -a -O--buildsystem=meson dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -a -O--buildsystem=meson dh_gencontrol -a -O--buildsystem=meson dh_md5sums -a -O--buildsystem=meson dh_builddeb -a -O--buildsystem=meson dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../blasr_5.3.5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../blasr_5.3.5+dfsg-1_amd64.changes dpkg-genchanges --build=any -O../blasr_5.3.5+dfsg-1_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 2021-12-06T18:02:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-1_amd64.changes: --------------------------------- Format: 1.8 Date: Mon, 11 Oct 2021 10:14:43 +0200 Source: blasr Binary: blasr blasr-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 5.3.5+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.5+dfsg-1) unstable; urgency=medium . * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Make sure version bumps will not break autopkgtest Checksums-Sha1: e1fbf96164f3272d22dee9535a81699cc8c8ca27 3165956 blasr-dbgsym_5.3.5+dfsg-1_amd64.deb e7aee50fe8f6d5f50273ec05bf1af40bf6de05fe 7437 blasr_5.3.5+dfsg-1_amd64.buildinfo f415942667c53b2db05280e2a129f96dd7d17c51 222568 blasr_5.3.5+dfsg-1_amd64.deb Checksums-Sha256: 46b2f9631ad7367e1a64e803d66ef3bf8b6eb726715a91b60bb7940f861975d5 3165956 blasr-dbgsym_5.3.5+dfsg-1_amd64.deb eca57d01fd561fcfb5b2c31b70c7d3b1246b1f6d893e01034a42b8e48988beba 7437 blasr_5.3.5+dfsg-1_amd64.buildinfo 3828308a12d3f1c9ebcd74e1656a7df2399ab97ced861fe38543160577c03b01 222568 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3165956 blasr-dbgsym_5.3.5+dfsg-1_amd64.deb 3828308a12d3f1c9ebcd74e1656a7df2399ab97ced861fe38543160577c03b01 222568 blasr_5.3.5+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Mon, 06 Dec 2021 18:02:49 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4), autotools-dev (= 20180224.1+nmu1), base-files (= 12), base-passwd (= 3.5.52), bash (= 5.1-5), binutils (= 2.37-10), binutils-aarch64-linux-gnu (= 2.37-10), binutils-common (= 2.37-10), bsdextrautils (= 2.37.2-4), bsdutils (= 1:2.37.2-4), build-essential (= 12.9), bzip2 (= 1.0.8-5), cmake (= 3.22.0-1), cmake-data (= 3.22.0-1), coreutils (= 8.32-4.1), cpp (= 4:11.2.0-2), cpp-11 (= 11.2.0-12), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2), debianutils (= 5.5-1), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9), dh-strip-nondeterminism (= 1.12.1-1), diffutils (= 1:3.7-5), dpkg (= 1.21.0), dpkg-dev (= 1.21.0), dwz (= 0.14-1), emacsen-common (= 3.0.4), file (= 1:5.41-2), findutils (= 4.8.0-1), g++ (= 4:11.2.0-2), g++-11 (= 11.2.0-12), gcc (= 4:11.2.0-2), gcc-11 (= 11.2.0-12), gcc-11-base (= 11.2.0-12), gettext (= 0.21-4), gettext-base (= 0.21-4), googletest (= 1.11.0-3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4), hdf5-helpers (= 1.10.7+repack-4), hostname (= 3.23), init-system-helpers (= 1.60), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2+b1), libasan6 (= 11.2.0-12), libatomic1 (= 11.2.0-12), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.6-1), libaudit1 (= 1:3.0.6-1+b1), libbinutils (= 2.37-10), libblasr-dev (= 5.3.5+dfsg-2), libblasr5.3.5 (= 5.3.5+dfsg-2), libblkid1 (= 2.37.2-4), libboost-dev (= 1.74.0.3), libboost1.74-dev (= 1.74.0-13), libbrotli1 (= 1.0.9-2+b3), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.32-5), libc-dev-bin (= 2.32-5), libc6 (= 2.32-5), libc6-dev (= 2.32-5), libcap-ng0 (= 0.7.9-2.2+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 11.2.0-12), libcom-err2 (= 1.46.4-1), libcrypt-dev (= 1:4.4.26-1), libcrypt1 (= 1:4.4.26-1), libctf-nobfd0 (= 2.37-10), libctf0 (= 2.37-10), libcurl3-gnutls (= 7.79.1-2), libcurl4 (= 7.79.1-2), libcurl4-gnutls-dev (= 7.79.1-2), libdb5.3 (= 5.3.28+dfsg1-0.8), libdebconfclient0 (= 0.261), libdebhelper-perl (= 13.5.2), libdeflate-dev (= 1.8-1), libdeflate0 (= 1.8-1), libdpkg-perl (= 1.21.0), libelf1 (= 0.186-1), libexpat1 (= 2.4.1-3), libffi8 (= 3.4.2-3), libfile-stripnondeterminism-perl (= 1.12.1-1), libgcc-11-dev (= 11.2.0-12), libgcc-s1 (= 11.2.0-12), libgcrypt20 (= 1.9.4-4), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgfortran5 (= 11.2.0-12), libglib2.0-0 (= 2.70.2-1), libgmp10 (= 2:6.2.1+dfsg-3), libgnutls30 (= 3.7.2-2), libgomp1 (= 11.2.0-12), libgpg-error0 (= 1.42-3), libgssapi-krb5-2 (= 1.18.3-7), libgtest-dev (= 1.11.0-3), libhdf5-103-1 (= 1.10.7+repack-4), libhdf5-cpp-103-1 (= 1.10.7+repack-4), libhdf5-dev (= 1.10.7+repack-4), libhdf5-fortran-102 (= 1.10.7+repack-4), libhdf5-hl-100 (= 1.10.7+repack-4), libhdf5-hl-cpp-100 (= 1.10.7+repack-4), libhdf5-hl-fortran-100 (= 1.10.7+repack-4), libhogweed6 (= 3.7.3-1), libhts-dev (= 1.13+ds-2), libhts3 (= 1.13+ds-2), libhtscodecs2 (= 1.1.1-3+b1), libicu67 (= 67.1-7), libidn2-0 (= 2.3.2-2), libisl23 (= 0.24-2), libitm1 (= 11.2.0-12), libjpeg-dev (= 1:2.1.2-1), libjpeg62-turbo (= 1:2.1.2-1), libjpeg62-turbo-dev (= 1:2.1.2-1), libjsoncpp24 (= 1.9.4-5), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), libldap-2.4-2 (= 2.4.59+dfsg-1), liblsan0 (= 11.2.0-12), liblz4-1 (= 1.9.3-2), liblzma-dev (= 5.2.5-2), liblzma5 (= 5.2.5-2), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmount1 (= 2.37.2-4), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.3-1), libncursesw6 (= 6.3-1), libnettle8 (= 3.7.3-1), libnghttp2-14 (= 1.43.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libp11-kit0 (= 0.24.0-6), libpam-modules (= 1.4.0-10), libpam-modules-bin (= 1.4.0-10), libpam-runtime (= 1.4.0-10), libpam0g (= 1.4.0-10), libpbbam-dev (= 1.6.0+dfsg-2), libpbbam1.6.0 (= 1.6.0+dfsg-2), libpbcopper-dev (= 1.9.3+dfsg-2), libpbcopper1.8.0 (= 1.8.0+dfsg-2+b1), libpbcopper1.9.3 (= 1.9.3+dfsg-2), libpbdata-dev (= 5.3.5+dfsg-2), libpbihdf-dev (= 5.3.5+dfsg-2), libpbseq-dev (= 5.3.5+dfsg-2), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.1-6), libpipeline1 (= 1.5.4-1), libprocps8 (= 2:3.3.17-5), libpsl5 (= 0.21.0-1.2), libpython3-stdlib (= 3.9.8-1), libpython3.9-minimal (= 3.9.9-1), libpython3.9-stdlib (= 3.9.9-1), libquadmath0 (= 11.2.0-12), libreadline8 (= 8.1-2), librhash0 (= 1.4.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.27+dfsg2-2), libsasl2-modules-db (= 2.1.27+dfsg2-2), libseccomp2 (= 2.5.3-2), libselinux1 (= 3.3-1+b1), libsigsegv2 (= 2.13-1), libsmartcols1 (= 2.37.2-4), libsqlite3-0 (= 3.36.0-2), libssh2-1 (= 1.10.0-2), libssl-dev (= 1.1.1l-1), libssl1.1 (= 1.1.1l-1), libstdc++-11-dev (= 11.2.0-12), libstdc++6 (= 11.2.0-12), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.7-1), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15), libtsan0 (= 11.2.0-12), libubsan1 (= 11.2.0-12), libuchardet0 (= 0.0.7-1), libudev1 (= 249.7-1), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4), libuv1 (= 1.42.0-1), libxml2 (= 2.9.12+dfsg-5+b1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.5-1), login (= 1:4.8.1-2), lsb-base (= 11.1.0), m4 (= 1.4.18-5), make (= 4.3-4.1), man-db (= 2.9.4-2), mawk (= 1.3.4.20200120-2), media-types (= 4.0.0), meson (= 0.60.2-1), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), ninja-build (= 1.10.1-1), patch (= 2.7.6-7), perl (= 5.32.1-6), perl-base (= 5.32.1-6), perl-modules-5.32 (= 5.32.1-6), pkg-config (= 0.29.2-1), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-5), python3 (= 3.9.8-1), python3-distutils (= 3.9.9-2), python3-lib2to3 (= 3.9.9-2), python3-minimal (= 3.9.8-1), python3-pkg-resources (= 59.4.0-1), python3.9 (= 3.9.9-1), python3.9-minimal (= 3.9.9-1), readline-common (= 8.1-2), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.00-1), tar (= 1.34+dfsg-1), tzdata (= 2021e-1), util-linux (= 2.37.2-4), xz-utils (= 5.2.5-2), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1633940083" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr-dbgsym_5.3.5+dfsg-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 3165956 bytes: control archive=640 bytes. 414 bytes, 12 lines control 294 bytes, 3 lines md5sums Package: blasr-dbgsym Source: blasr Version: 5.3.5+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3229 Depends: blasr (= 5.3.5+dfsg-1) Section: debug Priority: optional Description: debug symbols for blasr Build-Ids: 8839f823fb84fea4d1e25691e8e64544e3cded9b 888d7a95c49793850964830e04c72483bda2b94c drwxr-xr-x root/root 0 2021-10-11 08:14 ./ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/debug/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/debug/.build-id/88/ -rw-r--r-- root/root 3117312 2021-10-11 08:14 ./usr/lib/debug/.build-id/88/39f823fb84fea4d1e25691e8e64544e3cded9b.debug -rw-r--r-- root/root 144904 2021-10-11 08:14 ./usr/lib/debug/.build-id/88/8d7a95c49793850964830e04c72483bda2b94c.debug drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 30280 2021-10-11 08:14 ./usr/lib/debug/.dwz/x86_64-linux-gnu/blasr.debug drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/doc/ lrwxrwxrwx root/root 0 2021-10-11 08:14 ./usr/share/doc/blasr-dbgsym -> blasr blasr_5.3.5+dfsg-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 222568 bytes: control archive=1192 bytes. 787 bytes, 14 lines control 982 bytes, 15 lines md5sums Package: blasr Version: 5.3.5+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 656 Depends: libblasr5.3.5 (>= 5.3.5+dfsg), libc6 (>= 2.32), libgcc-s1 (>= 3.0), libhdf5-cpp-103-1 (>= 1.10.5), libpbbam1.6.0 (>= 1.6.0+dfsg), libpbcopper1.9.3 (>= 1.9.3+dfsg), libstdc++6 (>= 11), libpbseq Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. drwxr-xr-x root/root 0 2021-10-11 08:14 ./ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/bin/ -rwxr-xr-x root/root 583312 2021-10-11 08:14 ./usr/bin/blasr -rwxr-xr-x root/root 56264 2021-10-11 08:14 ./usr/bin/sawriter drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/doc/blasr/ -rw-r--r-- root/root 373 2021-10-11 08:14 ./usr/share/doc/blasr/NEWS.Debian.gz -rw-r--r-- root/root 1291 2021-02-18 10:03 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 208 2021-10-11 08:14 ./usr/share/doc/blasr/README.source -rw-r--r-- root/root 542 2021-10-11 08:14 ./usr/share/doc/blasr/README.test -rw-r--r-- root/root 41 2021-10-11 08:14 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 2173 2021-10-11 08:14 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2193 2021-10-11 08:14 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/doc/blasr/examples/ -rw-r--r-- root/root 65 2021-10-11 08:14 ./usr/share/doc/blasr/examples/query.fasta -rw-r--r-- root/root 72 2021-10-11 08:14 ./usr/share/doc/blasr/examples/ref.fa -rw-r--r-- root/root 897 2021-10-11 08:14 ./usr/share/doc/blasr/run-unit-test drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/lintian/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 84 2021-10-11 08:14 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/man/ drwxr-xr-x root/root 0 2021-10-11 08:14 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2021-10-11 08:14 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2021-10-11 08:14 ./usr/share/man/man1/sawriter.1.gz 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 [624 B] Get:5 copy:/<>/apt_archive ./ Packages [714 B] Fetched 2301 B in 0s (53.7 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: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-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 liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-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-glob-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 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libwww-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg liblist-someutils-xs-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-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 libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libio-interactive-perl libio-prompt-tiny-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 liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-ipv6addr-perl libnet-netmask-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-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-glob-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 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. Need to get 6627 kB of archives. After this operation, 20.6 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 diffstat arm64 1.64-1 [34.6 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-1 [49.3 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.27-2 [540 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.27-2 [883 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-1.1 [14.1 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40 [69.4 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-1+b3 [11.2 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b2 [15.8 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-1+b3 [25.5 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.31-1 [24.2 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-1.1 [12.4 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:16 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-1+b3 [44.2 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.25-1 [19.5 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:20 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-3+b7 [36.9 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b1 [15.3 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.27-1 [17.1 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b1 [25.3 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-1.1 [10.8 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-1.1 [8552 B] Get:29 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.27-1 [126 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-1.1 [18.4 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-1.1 [13.7 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-2 [36.8 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.01-2 [34.3 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-1.1 [33.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-1+b5 [103 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-1 [10.7 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-1+b2 [25.8 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.04-1+b3 [26.7 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B] Get:51 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B] Get:52 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-1.1 [318 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-1.1 [21.3 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libio-prompt-tiny-perl all 0.003-1 [9150 B] Get:58 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.11-1 [15.4 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:65 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:66 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-1.1 [10.8 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b1 [170 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.39-1 [21.9 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-1+b3 [11.9 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-1+b1 [13.5 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.120-1 [54.7 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.19-1+b7 [17.0 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.008-1+b1 [11.8 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1 [46.1 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.018+ds-1+b1 [95.3 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.018+ds-1+b1 [98.3 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-1 [11.0 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.21-1 [49.8 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.26-1 [28.4 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-1+b2 [27.3 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-4+b8 [8680 B] Get:86 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1 [13.1 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1 [195 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-1+b3 [75.1 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b2 [19.8 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.10-1 [91.0 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1 [34.2 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 lzip arm64 1.22-4 [84.6 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-26 [165 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 lintian all 2.114.0 [1382 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6627 kB in 0s (35.7 MB/s) Selecting previously unselected package diffstat. (Reading database ... 40677 files and directories currently installed.) Preparing to unpack .../00-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../01-libassuan0_2.5.5-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../02-gpgconf_2.2.27-2_arm64.deb ... Unpacking gpgconf (2.2.27-2) ... Selecting previously unselected package gpg. Preparing to unpack .../03-gpg_2.2.27-2_arm64.deb ... Unpacking gpg (2.2.27-2) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../04-libaliased-perl_0.34-1.1_all.deb ... Unpacking libaliased-perl (0.34-1.1) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../05-libapt-pkg-perl_0.1.40_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../06-libb-hooks-op-check-perl_0.22-1+b3_arm64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b3) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../07-libdynaloader-functions-perl_0.003-1.1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1.1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../08-libdevel-callchecker-perl_0.008-1+b2_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b2) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../09-libparams-classify-perl_0.015-1+b3_arm64.deb ... Unpacking libparams-classify-perl (0.015-1+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../10-libmodule-runtime-perl_0.016-1_all.deb ... Unpacking libmodule-runtime-perl (0.016-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../11-libtry-tiny-perl_0.31-1_all.deb ... Unpacking libtry-tiny-perl (0.31-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../12-libmodule-implementation-perl_0.09-1.1_all.deb ... Unpacking libmodule-implementation-perl (0.09-1.1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../13-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../14-libvariable-magic-perl_0.62-1+b3_arm64.deb ... Unpacking libvariable-magic-perl (0.62-1+b3) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../15-libb-hooks-endofscope-perl_0.25-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.25-1) ... Selecting previously unselected package libcapture-tiny-perl. 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Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-1+b3) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up liblist-moreutils-xs-perl (0.430-2) ... Setting up libparams-util-perl (1.102-1+b1) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:arm64 (3.5.9-1) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl (0.26-1+b1) ... Setting up libsyntax-keyword-try-perl (0.26-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.634-1) ... Setting up libpath-tiny-perl (0.120-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.27-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libaliased-perl (0.34-1.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b7) ... Setting up libsort-versions-perl (1.62-1) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-1+b2) ... Setting up libfont-ttf-perl (1.06-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-4+b8) ... Setting up libperlio-gzip-perl (0.19-1+b7) ... Setting up libhtml-html5-entities-perl (0.004-1.1) ... Setting up libsereal-decoder-perl (4.018+ds-1+b1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.10-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.27-2) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.04-1+b3) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libtext-markdown-discount-perl:arm64 (0.13-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libdata-validate-uri-perl (0.07-1) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libiterator-perl (0.03+ds1-1.1) ... Setting up libiterator-util-perl (0.02+ds1-1.1) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libconst-fast-perl (0.014-1.1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1.1) ... Setting up libpackage-stash-perl (0.39-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-1.1) ... Setting up libb-hooks-endofscope-perl (0.25-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.114.0) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.32-5) ... 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: 119264 Build-Time: 476 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 92 Job: blasr_5.3.5+dfsg-1 Lintian: pass Machine Architecture: arm64 Package: blasr Package-Time: 599 Source-Version: 5.3.5+dfsg-1 Space: 119264 Status: successful Version: 5.3.5+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-12-06T18:02:51Z Build needed 00:09:59, 119264k disk space