I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 25 01:43:03 -12 2025 I: pbuilder-time-stamp: 1745588583 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [genomicsdb_1.5.4-5.dsc] I: copying [./genomicsdb_1.5.4.orig-genomicsdb-htslib.tar.gz] I: copying [./genomicsdb_1.5.4.orig-genomicsdb-tiledb.tar.gz] I: copying [./genomicsdb_1.5.4.orig.tar.gz] I: copying [./genomicsdb_1.5.4-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./genomicsdb_1.5.4-5.dsc: unsupported subcommand dpkg-source: info: extracting genomicsdb in genomicsdb-1.5.4 dpkg-source: info: unpacking genomicsdb_1.5.4.orig.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.4.orig-genomicsdb-htslib.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.4.orig-genomicsdb-tiledb.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.4-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_download_of_dependencies.patch dpkg-source: info: applying using_htslib_from_component.patch dpkg-source: info: applying using_timedb_from_component.patch dpkg-source: info: applying strip_tiledb_CMakeLists.patch dpkg-source: info: applying ignoring_sdk_to_download.patch dpkg-source: info: applying use_shared_protobuf_lib.patch dpkg-source: info: applying missing_links_in_libs.patch dpkg-source: info: applying pom.patch dpkg-source: info: applying no_spark_in_Java_build.patch dpkg-source: info: applying tests_in_all_target.patch dpkg-source: info: applying run_tests_in_not_yet_installed_dir.patch dpkg-source: info: applying build_jni.patch dpkg-source: info: applying library_names_and_install_paths.patch dpkg-source: info: applying htslib_define_PATH_MAX.patch dpkg-source: info: applying htslib_testShebang.patch dpkg-source: info: applying htslib_fix_float_precision dpkg-source: info: applying handling_rpaths.patch dpkg-source: info: applying disabling_mpi_for_tests.patch dpkg-source: info: applying JsonFormat_from_libprotobuf-java.patch dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying catch2_3.patch dpkg-source: info: applying variant_array_schema_hidden_if_no_DEBUG.patch dpkg-source: info: applying rapidjson_methods.patch dpkg-source: info: applying query_config_serialization.patch dpkg-source: info: applying fmt10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/811065/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b2daeb80acd54a39b004cfc68ce0251c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='811065' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gb82VezV/pbuilderrc_pE4U --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gb82VezV/b1 --logfile b1/build.log genomicsdb_1.5.4-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/811065/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, default-jdk, javahelper, libbz2-dev, libcatch2-dev, libcurlpp-dev, libfmt-dev, libmuparserx-dev, libprotobuf-dev, libspdlog-dev, libssl-dev, liblzma-dev, maven-debian-helper, mpi-default-dev, protobuf-compiler, rapidjson-dev, testng, uuid-dev, libbuild-helper-maven-plugin-java, libcommons-io-java, libcommons-lang3-java, libgetopt-java, libguava-java, libhtsjdk-java, libjson-simple-java, liblog4j2-java, libmaven-antrun-plugin-java, libprotobuf-java, libsurefire-java, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19954 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcatch2-dev; however: Package libcatch2-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurlpp-dev; however: Package libcurlpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libfmt-dev; however: Package libfmt-dev is not installed. pbuilder-satisfydepends-dummy depends on libmuparserx-dev; however: Package libmuparserx-dev is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on maven-debian-helper; however: Package maven-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on testng; however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on uuid-dev; however: Package uuid-dev is not installed. pbuilder-satisfydepends-dummy depends on libbuild-helper-maven-plugin-java; however: Package libbuild-helper-maven-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-io-java; however: Package libcommons-io-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-lang3-java; however: Package libcommons-lang3-java is not installed. pbuilder-satisfydepends-dummy depends on libgetopt-java; however: Package libgetopt-java is not installed. pbuilder-satisfydepends-dummy depends on libguava-java; however: Package libguava-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on libjson-simple-java; however: Package libjson-simple-java is not installed. pbuilder-satisfydepends-dummy depends on liblog4j2-java; however: Package liblog4j2-java is not installed. pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however: Package libmaven-antrun-plugin-java is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-java; however: Package libprotobuf-java is not installed. pbuilder-satisfydepends-dummy depends on libsurefire-java; however: Package libsurefire-java is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} ant{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} chrpath{a} cmake{a} cmake-data{a} comerr-dev{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gpg{a} gpg-agent{a} gpgconf{a} gpgv{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} ibverbs-providers{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} junit4{a} junit5{a} krb5-multidev{a} libamd-comgr2{a} libamdhip64-5{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libapparmor1{a} libarchive-zip-perl{a} libarchive13t64{a} libasm-java{a} libasound2-data{a} libasound2t64{a} libassuan9{a} libatinject-jsr330-api-java{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli-dev{a} libbrotli1{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbz2-dev{a} libcairo-gobject2{a} libcairo2{a} libcatch2-dev{a} libcbor0.10{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcloudproviders0{a} libcolord2{a} libcom-err2{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-digester-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libcups2t64{a} libcurl4-openssl-dev{a} libcurl4t64{a} libcurlpp-dev{a} libcurlpp0t64{a} libdatrie1{a} libdbus-1-3{a} libdconf1{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1t64{a} libencode-locale-perl{a} libepoxy0{a} liberror-prone-java{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libezmorph-java{a} libfabric1{a} libffi8{a} libfido2-1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfmt-dev{a} libfmt10{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgcrypt20{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgetopt-java{a} libgfortran-14-dev{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgoogle-gson-java{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtk-3-0t64{a} libgtk-3-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs-dev{a} libibverbs1{a} libidn2-0{a} libidn2-dev{a} libimport-into-perl{a} libio-html-perl{a} libio-socket-ssl-perl{a} libjansi-java{a} libjaxen-java{a} libjbig0{a} libjcommander-java{a} libjetty9-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjson-java{a} libjson-simple-java{a} libjsoncpp26{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblcms2-2{a} libldap-dev{a} libldap2{a} liblerc4{a} liblightcouch-java{a} libllvm17t64{a} libllvm19{a} liblog4j2-java{a} libltdl-dev{a} libltdl7{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-jar-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven3-core-java{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmunge2{a} libmuparserx-dev{a} libmuparserx4.0.12{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngs-java{a} libngs-jni{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnpth0t64{a} libnspr4{a} libnss3{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi40{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libp11-kit-dev{a} libp11-kit0{a} libpam-systemd{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libplexus-xml-java{a} libpmix-dev{a} libpmix2t64{a} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqdox2-java{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librhino-java{a} librole-tiny-perl{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsharpyuv0{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspdlog-dev{a} libspdlog1.15{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsub-quote-perl{a} libsurefire-java{a} libsystemd-shared{a} libtasn1-6{a} libtasn1-6-dev{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libucx0{a} libunbound8{a} libunistring5{a} libunivocity-parsers-java{a} liburi-perl{a} libuv1t64{a} libvelocity-tools-java{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxkbcommon0{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxnvctrl0{a} libxom-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} mesa-libgallium{a} mpi-default-dev{a} ncbi-vdb-data{a} netbase{a} nettle-dev{a} ocl-icd-libopencl1{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.13{a} python3.13-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sopv-gpgv{a} systemd{a} systemd-sysv{a} testng{a} tzdata{a} unzip{a} uuid-dev{a} velocity{a} wdiff{a} x11-common{a} xkb-data{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional at-spi2-core bzip2-doc chrony curl debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra gnupg javascript-common krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libcoarrays-openmpi-dev libdata-dump-perl libdistro-info-perl libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpg-error-l10n libgtk-3-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libkmod2 libldap-common liblist-compare-perl libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnss-systemd librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libtasn1-doc libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian linux-sysctl-defaults lynx lzip mesa-vulkan-drivers ntpsec openntpd pristine-tar psmisc publicsuffix python3-apt python3-argcomplete python3-debian python3-magic python3-requests python3-unidiff python3-xdg sopv-doc strace systemd-cryptsetup systemd-timesyncd wget xauth xdg-user-dirs 0 packages upgraded, 491 newly installed, 0 to remove and 0 not upgraded. Need to get 368 MB of archives. After unpacking 1246 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libsystemd-shared arm64 257.5-2 [1911 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libapparmor1 arm64 4.1.0-1 [42.9 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 systemd arm64 257.5-2 [2920 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 systemd-sysv arm64 257.5-2 [63.9 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 libdbus-1-3 arm64 1.16.2-2 [169 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 dbus-bin arm64 1.16.2-2 [78.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 dbus-daemon arm64 1.16.2-2 [152 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 dbus arm64 1.16.2-2 [70.7 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 binfmt-support arm64 2.2.2-7+b1 [68.2 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.13.2-2 [27.1 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 media-types all 13.0.0 [29.3 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 netbase all 6.5 [12.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 tzdata all 2025b-2 [260 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.13.2-2 [10.1 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.13.2-2 [28.1 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.5.0-1 [1454 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libpam-systemd arm64 257.5-2 [275 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-2 [27.4 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.15.0-1+b1 [74.3 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.9p2-2 [906 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-2 [311 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.84.1-1 [1423 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 shared-mime-info arm64 2.4-5+b2 [756 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.47-1.1 [274 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.7.0-3 [325 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.12+dfsg-2 [131 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 gtk-update-icon-cache arm64 4.18.4+ds-1 [51.2 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 adwaita-icon-theme all 48.0-1 [504 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 java-common all 0.76 [6776 B] Get: 70 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.110-1 [1292 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.3.3-1 [55.0 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jre-headless arm64 21.0.7~8ea-1 [40.6 MB] Get: 75 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 76 http://deb.debian.org/debian trixie/main arm64 ant all 1.10.15-1 [2163 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 at-spi2-common all 2.56.1-2 [171 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-4 [862 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 chrpath arm64 0.18-1 [13.2 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.31.6-2 [2268 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.13.0-1 [348 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.31.6-2 [9906 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1+b1 [56.2 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 dbus-user-session arm64 1.16.2-2 [52.1 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libdconf1 arm64 0.40.0-5 [40.4 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 dconf-service arm64 0.40.0-5 [30.9 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 dconf-gsettings-backend arm64 0.40.0-5 [27.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 dctrl-tools arm64 2.24-3+b1 [125 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-4 [539 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 117 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.2 [919 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libatk1.0-0t64 arm64 2.56.1-2 [50.0 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.12-1 [795 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libatspi2.0-0t64 arm64 2.56.1-2 [76.5 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libatk-bridge2.0-0t64 arm64 2.56.1-2 [64.8 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-2.3 [318 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-2.3 [387 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.12-1 [27.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.4-1+b1 [483 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libcairo-gobject2 arm64 1.18.4-1+b1 [130 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libcloudproviders0 arm64 0.3.6-2 [27.4 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 libcolord2 arm64 1.4.7-3 [130 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 libavahi-common-data arm64 0.8-16 [112 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libavahi-common3 arm64 0.8-16 [43.3 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libavahi-client3 arm64 0.8-16 [46.7 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libcups2t64 arm64 2.4.10-2+b1 [236 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libepoxy0 arm64 1.5.10-2 [200 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 10.2.0-1+b1 [442 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-2.3 [463 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.56.3-1 [213 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [52.9 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [33.7 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libwayland-client0 arm64 1.23.1-3 [26.1 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libwayland-cursor0 arm64 1.23.1-3 [11.7 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libwayland-egl1 arm64 1.23.1-3 [5952 B] Get: 164 http://deb.debian.org/debian trixie/main arm64 libxcomposite1 arm64 1:0.4.6-1 [16.4 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libxfixes3 arm64 1:6.0.0-2+b4 [20.5 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libxcursor1 arm64 1:1.2.3-1 [39.3 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libxdamage1 arm64 1:1.1.6-1+b2 [15.6 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libxinerama1 arm64 2:1.1.4-3+b4 [16.0 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 xkb-data all 2.42-1 [790 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libxkbcommon0 arm64 1.7.0-2 [106 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libxrandr2 arm64 2:1.5.4-1+b3 [35.9 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libgtk-3-common all 3.24.49-3 [4908 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libgtk-3-0t64 arm64 3.24.49-3 [2565 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libglvnd0 arm64 1.7.0-1+b2 [41.6 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libdrm-common all 2.4.124-2 [8288 B] Get: 176 http://deb.debian.org/debian trixie/main arm64 libdrm2 arm64 2.4.124-2 [38.3 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 libx11-xcb1 arm64 2:1.8.12-1 [247 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libxcb-dri3-0 arm64 1.17.0-2+b1 [107 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 libxcb-glx0 arm64 1.17.0-2+b1 [123 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libxcb-present0 arm64 1.17.0-2+b1 [106 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libxcb-xfixes0 arm64 1.17.0-2+b1 [110 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b4 [19.2 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libdrm-amdgpu1 arm64 2.4.124-2 [21.8 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libz3-4 arm64 4.13.3-1 [7507 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libllvm19 arm64 1:19.1.7-3 [23.3 MB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libsensors5 arm64 1:3.6.2-2 [36.4 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libxcb-randr0 arm64 1.17.0-2+b1 [117 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libxcb-sync1 arm64 1.17.0-2+b1 [109 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 libxshmfence1 arm64 1.3.3-1 [11.1 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 mesa-libgallium arm64 25.0.3-1 [8027 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 libwayland-server0 arm64 1.23.1-3 [33.7 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 libgbm1 arm64 25.0.3-1 [43.5 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 libvulkan1 arm64 1.4.309.0-1 [127 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 libgl1-mesa-dri arm64 25.0.3-1 [45.3 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 libglx-mesa0 arm64 25.0.3-1 [142 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 libglx0 arm64 1.7.0-1+b2 [31.1 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 libgl1 arm64 1.7.0-1+b2 [90.9 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 libasound2-data all 1.2.14-1 [21.1 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 libasound2t64 arm64 1.2.14-1 [342 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 libxtst6 arm64 2:1.2.5-1 [25.7 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jre arm64 21.0.7~8ea-1 [193 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 default-jre arm64 2:1.21-76 [1068 B] Get: 206 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jdk-headless arm64 21.0.7~8ea-1 [81.9 MB] Get: 207 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 208 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jdk arm64 21.0.7~8ea-1 [3549 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 default-jdk arm64 2:1.21-76 [1076 B] Get: 210 http://deb.debian.org/debian trixie/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 213 http://deb.debian.org/debian trixie/main arm64 gpgconf arm64 2.2.46-6 [115 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 gpg arm64 2.2.46-6 [483 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 pinentry-curses arm64 1.3.1-2 [83.5 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 gpg-agent arm64 2.2.46-6 [231 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 gpgv arm64 2.2.46-6 [202 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 sopv-gpgv all 0.1.4-1 [11.3 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 221 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 libfile-touch-perl all 0.12-2 [8816 B] Get: 224 http://deb.debian.org/debian trixie/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get: 227 http://deb.debian.org/debian trixie/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 228 http://deb.debian.org/debian trixie/main arm64 libdevel-callchecker-perl arm64 0.009-1+b1 [16.3 kB] Get: 229 http://deb.debian.org/debian trixie/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get: 230 http://deb.debian.org/debian trixie/main arm64 libmodule-runtime-perl all 0.017-1 [17.9 kB] Get: 231 http://deb.debian.org/debian trixie/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 232 http://deb.debian.org/debian trixie/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 233 http://deb.debian.org/debian trixie/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 234 http://deb.debian.org/debian trixie/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 235 http://deb.debian.org/debian trixie/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 236 http://deb.debian.org/debian trixie/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 237 http://deb.debian.org/debian trixie/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 238 http://deb.debian.org/debian trixie/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 239 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 240 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 241 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get: 242 http://deb.debian.org/debian trixie/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 243 http://deb.debian.org/debian trixie/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get: 244 http://deb.debian.org/debian trixie/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get: 245 http://deb.debian.org/debian trixie/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 246 http://deb.debian.org/debian trixie/main arm64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 247 http://deb.debian.org/debian trixie/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 248 http://deb.debian.org/debian trixie/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 249 http://deb.debian.org/debian trixie/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get: 250 http://deb.debian.org/debian trixie/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get: 251 http://deb.debian.org/debian trixie/main arm64 libio-socket-ssl-perl all 2.089-1 [223 kB] Get: 252 http://deb.debian.org/debian trixie/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 253 http://deb.debian.org/debian trixie/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 254 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 255 http://deb.debian.org/debian trixie/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 256 http://deb.debian.org/debian trixie/main arm64 libwww-perl all 6.78-1 [183 kB] Get: 257 http://deb.debian.org/debian trixie/main arm64 patchutils arm64 0.4.2-1+b1 [71.3 kB] Get: 258 http://deb.debian.org/debian trixie/main arm64 wdiff arm64 1.2.2-8 [122 kB] Get: 259 http://deb.debian.org/debian trixie/main arm64 devscripts all 2.25.9 [1057 kB] Get: 260 http://deb.debian.org/debian trixie/main arm64 fastjar arm64 2:0.98-7+b1 [74.9 kB] Get: 261 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 262 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-19 [418 kB] Get: 263 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-19 [9794 kB] Get: 264 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-19 [14.5 kB] Get: 265 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-2 [57.1 kB] Get: 266 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-2 [167 kB] Get: 267 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 56.1-1 [58.9 kB] Get: 268 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 56.1-1 [333 kB] Get: 269 http://deb.debian.org/debian trixie/main arm64 jarwrapper all 0.80 [9692 B] Get: 270 http://deb.debian.org/debian trixie/main arm64 javahelper all 0.80 [80.4 kB] Get: 271 http://deb.debian.org/debian trixie/main arm64 libhamcrest-java all 2.2-2 [121 kB] Get: 272 http://deb.debian.org/debian trixie/main arm64 junit4 all 4.13.2-5 [350 kB] Get: 273 http://deb.debian.org/debian trixie/main arm64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 274 http://deb.debian.org/debian trixie/main arm64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 275 http://deb.debian.org/debian trixie/main arm64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 276 http://deb.debian.org/debian trixie/main arm64 libpicocli-java all 4.6.2-2 [390 kB] Get: 277 http://deb.debian.org/debian trixie/main arm64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 278 http://deb.debian.org/debian trixie/main arm64 junit5 all 5.10.3-1 [2459 kB] Get: 279 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 280 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 281 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 282 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 283 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 284 http://deb.debian.org/debian trixie/main arm64 libllvm17t64 arm64 1:17.0.6-21+b1 [21.3 MB] Get: 285 http://deb.debian.org/debian trixie/main arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3+b2 [12.1 MB] Get: 286 http://deb.debian.org/debian trixie/main arm64 libnuma1 arm64 2.0.18-1+b1 [21.8 kB] Get: 287 http://deb.debian.org/debian trixie/main arm64 libhsakmt1 arm64 6.2.4+ds-1 [58.3 kB] Get: 288 http://deb.debian.org/debian trixie/main arm64 libhsa-runtime64-1 arm64 6.1.2-3 [302 kB] Get: 289 http://deb.debian.org/debian trixie/main arm64 libamdhip64-5 arm64 5.7.1-5+b1 [8826 kB] Get: 290 http://deb.debian.org/debian trixie/main arm64 libaopalliance-java all 20070526-7 [8572 B] Get: 291 http://deb.debian.org/debian trixie/main arm64 libapache-pom-java all 33-2 [5852 B] Get: 292 http://deb.debian.org/debian trixie/main arm64 libasm-java all 9.7.1-1 [391 kB] Get: 293 http://deb.debian.org/debian trixie/main arm64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 294 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 295 http://deb.debian.org/debian trixie/main arm64 libbsh-java all 2.0b4-20 [291 kB] Get: 296 http://deb.debian.org/debian trixie/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 297 http://deb.debian.org/debian trixie/main arm64 libcommons-io-java all 2.18.0-1 [509 kB] Get: 298 http://deb.debian.org/debian trixie/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 299 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 300 http://deb.debian.org/debian trixie/main arm64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 301 http://deb.debian.org/debian trixie/main arm64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 302 http://deb.debian.org/debian trixie/main arm64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 303 http://deb.debian.org/debian trixie/main arm64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 304 http://deb.debian.org/debian trixie/main arm64 libguava-java all 32.0.1-1 [2708 kB] Get: 305 http://deb.debian.org/debian trixie/main arm64 libguice-java all 5.1.0-1 [932 kB] Get: 306 http://deb.debian.org/debian trixie/main arm64 libmaven-parent-java all 43-2 [6252 B] Get: 307 http://deb.debian.org/debian trixie/main arm64 libcommons-lang3-java all 3.17.0-1 [641 kB] Get: 308 http://deb.debian.org/debian trixie/main arm64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 309 http://deb.debian.org/debian trixie/main arm64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 310 http://deb.debian.org/debian trixie/main arm64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 311 http://deb.debian.org/debian trixie/main arm64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 312 http://deb.debian.org/debian trixie/main arm64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 313 http://deb.debian.org/debian trixie/main arm64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 314 http://deb.debian.org/debian trixie/main arm64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 315 http://deb.debian.org/debian trixie/main arm64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 316 http://deb.debian.org/debian trixie/main arm64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 317 http://deb.debian.org/debian trixie/main arm64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 318 http://deb.debian.org/debian trixie/main arm64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 319 http://deb.debian.org/debian trixie/main arm64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 320 http://deb.debian.org/debian trixie/main arm64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 321 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 322 http://deb.debian.org/debian trixie/main arm64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 323 http://deb.debian.org/debian trixie/main arm64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 324 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 325 http://deb.debian.org/debian trixie/main arm64 libcatch2-dev arm64 3.7.1-0.5 [588 kB] Get: 326 http://deb.debian.org/debian trixie/main arm64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 327 http://deb.debian.org/debian trixie/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 328 http://deb.debian.org/debian trixie/main arm64 libcommons-beanutils-java all 1.9.4-2 [233 kB] Get: 329 http://deb.debian.org/debian trixie/main arm64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 330 http://deb.debian.org/debian trixie/main arm64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 331 http://deb.debian.org/debian trixie/main arm64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 332 http://deb.debian.org/debian trixie/main arm64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 333 http://deb.debian.org/debian trixie/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 334 http://deb.debian.org/debian trixie/main arm64 libcommons-lang-java all 2.6-10 [273 kB] Get: 335 http://deb.debian.org/debian trixie/main arm64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 336 http://deb.debian.org/debian trixie/main arm64 libsnappy1v5 arm64 1.2.2-1 [28.3 kB] Get: 337 http://deb.debian.org/debian trixie/main arm64 libsnappy-jni arm64 1.1.10.7-1 [6476 B] Get: 338 http://deb.debian.org/debian trixie/main arm64 libsnappy-java all 1.1.10.7-1 [87.6 kB] Get: 339 http://deb.debian.org/debian trixie/main arm64 libxz-java all 1.9-1 [143 kB] Get: 340 http://deb.debian.org/debian trixie/main arm64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 341 http://deb.debian.org/debian trixie/main arm64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 342 http://deb.debian.org/debian trixie/main arm64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 343 http://deb.debian.org/debian trixie/main arm64 libcommons-text-java all 1.13.0-1 [228 kB] Get: 344 http://deb.debian.org/debian trixie/main arm64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 345 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.8-2 [101 kB] Get: 346 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 347 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-2 [305 kB] Get: 348 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 349 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 350 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 351 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 352 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 353 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 354 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 355 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 356 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 357 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 358 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 359 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 360 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 361 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 362 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 363 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 364 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 365 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 366 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.5.0-1 [3383 kB] Get: 367 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 368 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.7+dfsg-1 [335 kB] Get: 369 http://deb.debian.org/debian trixie/main arm64 libcurl4-openssl-dev arm64 8.13.0-1 [479 kB] Get: 370 http://deb.debian.org/debian trixie/main arm64 libcurlpp0t64 arm64 0.8.1-6 [26.1 kB] Get: 371 http://deb.debian.org/debian trixie/main arm64 libcurlpp-dev arm64 0.8.1-6 [58.3 kB] Get: 372 http://deb.debian.org/debian trixie/main arm64 libjaxen-java all 1.1.6-5 [214 kB] Get: 373 http://deb.debian.org/debian trixie/main arm64 libdom4j-java all 2.1.4-1 [312 kB] Get: 374 http://deb.debian.org/debian trixie/main arm64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 375 http://deb.debian.org/debian trixie/main arm64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 376 http://deb.debian.org/debian trixie/main arm64 libdoxia-java all 2.0.0-1 [113 kB] Get: 377 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 378 http://deb.debian.org/debian trixie/main arm64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 379 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 380 http://deb.debian.org/debian trixie/main arm64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 381 http://deb.debian.org/debian trixie/main arm64 velocity all 1.7-7 [431 kB] Get: 382 http://deb.debian.org/debian trixie/main arm64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 383 http://deb.debian.org/debian trixie/main arm64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 384 http://deb.debian.org/debian trixie/main arm64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 385 http://deb.debian.org/debian trixie/main arm64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 386 http://deb.debian.org/debian trixie/main arm64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 387 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-10+b1 [126 kB] Get: 388 http://deb.debian.org/debian trixie/main arm64 libevent-extra-2.1-7t64 arm64 2.1.12-stable-10+b1 [102 kB] Get: 389 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10+b1 [54.4 kB] Get: 390 http://deb.debian.org/debian trixie/main arm64 libevent-openssl-2.1-7t64 arm64 2.1.12-stable-10+b1 [60.4 kB] Get: 391 http://deb.debian.org/debian trixie/main arm64 libevent-dev arm64 2.1.12-stable-10+b1 [304 kB] Get: 392 http://deb.debian.org/debian trixie/main arm64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 393 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 56.1-1 [67.2 kB] Get: 394 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3.1 [480 kB] Get: 395 http://deb.debian.org/debian trixie/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 396 http://deb.debian.org/debian trixie/main arm64 libfmt-dev arm64 10.1.1+ds1-4 [177 kB] Get: 397 http://deb.debian.org/debian trixie/main arm64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get: 398 http://deb.debian.org/debian trixie/main arm64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 399 http://deb.debian.org/debian trixie/main arm64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 400 http://deb.debian.org/debian trixie/main arm64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 401 http://deb.debian.org/debian trixie/main arm64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 402 http://deb.debian.org/debian trixie/main arm64 libxom-java all 1.3.9-1 [174 kB] Get: 403 http://deb.debian.org/debian trixie/main arm64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 404 http://deb.debian.org/debian trixie/main arm64 libmbedcrypto16 arm64 3.6.3-1 [343 kB] Get: 405 http://deb.debian.org/debian trixie/main arm64 libmbedx509-7 arm64 3.6.3-1 [148 kB] Get: 406 http://deb.debian.org/debian trixie/main arm64 libmbedtls21 arm64 3.6.3-1 [224 kB] Get: 407 http://deb.debian.org/debian trixie/main arm64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 408 http://deb.debian.org/debian trixie/main arm64 libncbi-vdb3 arm64 3.2.1+dfsg-2 [1096 kB] Get: 409 http://deb.debian.org/debian trixie/main arm64 libncbi-ngs3 arm64 3.2.1+dfsg-3 [145 kB] Get: 410 http://deb.debian.org/debian trixie/main arm64 libngs-jni arm64 3.2.1+dfsg-3 [27.6 kB] Get: 411 http://deb.debian.org/debian trixie/main arm64 libngs-java arm64 3.2.1+dfsg-3 [114 kB] Get: 412 http://deb.debian.org/debian trixie/main arm64 librhino-java all 1.7.15-1 [1382 kB] Get: 413 http://deb.debian.org/debian trixie/main arm64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 414 http://deb.debian.org/debian trixie/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 415 http://deb.debian.org/debian trixie/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 416 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.12.0-1 [142 kB] Get: 417 http://deb.debian.org/debian trixie/main arm64 libnuma-dev arm64 2.0.18-1+b1 [37.8 kB] Get: 418 http://deb.debian.org/debian trixie/main arm64 libltdl7 arm64 2.5.4-4 [415 kB] Get: 419 http://deb.debian.org/debian trixie/main arm64 libltdl-dev arm64 2.5.4-4 [168 kB] Get: 420 http://deb.debian.org/debian trixie/main arm64 libhwloc-dev arm64 2.12.0-1 [238 kB] Get: 421 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b3 [51.2 kB] Get: 422 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1+b2 [14.0 kB] Get: 423 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.3-1 [42.7 kB] Get: 424 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.12.0-1 [17.8 kB] Get: 425 http://deb.debian.org/debian trixie/main arm64 libibumad3 arm64 56.1-1 [28.6 kB] Get: 426 http://deb.debian.org/debian trixie/main arm64 libibmad5 arm64 56.1-1 [42.4 kB] Get: 427 http://deb.debian.org/debian trixie/main arm64 libnl-3-dev arm64 3.7.0-2 [102 kB] Get: 428 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-dev arm64 3.7.0-2 [199 kB] Get: 429 http://deb.debian.org/debian trixie/main arm64 libibverbs-dev arm64 56.1-1 [642 kB] Get: 430 http://deb.debian.org/debian trixie/main arm64 libjansi-java all 2.4.1-2 [100 kB] Get: 431 http://deb.debian.org/debian trixie/main arm64 libjcommander-java all 1.71-4 [73.0 kB] Get: 432 http://deb.debian.org/debian trixie/main arm64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 433 http://deb.debian.org/debian trixie/main arm64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 434 http://deb.debian.org/debian trixie/main arm64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 435 http://deb.debian.org/debian trixie/main arm64 libjetty9-java all 9.4.57-1 [2965 kB] Get: 436 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 437 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 438 http://deb.debian.org/debian trixie/main arm64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 439 http://deb.debian.org/debian trixie/main arm64 libjsoup-java all 1.15.3-1 [431 kB] Get: 440 http://deb.debian.org/debian trixie/main arm64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 441 http://deb.debian.org/debian trixie/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 442 http://deb.debian.org/debian trixie/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 443 http://deb.debian.org/debian trixie/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 444 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.8.1-1 [344 kB] Get: 445 http://deb.debian.org/debian trixie/main arm64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 446 http://deb.debian.org/debian trixie/main arm64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 447 http://deb.debian.org/debian trixie/main arm64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 448 http://deb.debian.org/debian trixie/main arm64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 449 http://deb.debian.org/debian trixie/main arm64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 450 http://deb.debian.org/debian trixie/main arm64 libqdox2-java all 2.0.3-1 [296 kB] Get: 451 http://deb.debian.org/debian trixie/main arm64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 452 http://deb.debian.org/debian trixie/main arm64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 453 http://deb.debian.org/debian trixie/main arm64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 454 http://deb.debian.org/debian trixie/main arm64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 455 http://deb.debian.org/debian trixie/main arm64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 456 http://deb.debian.org/debian trixie/main arm64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 457 http://deb.debian.org/debian trixie/main arm64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 458 http://deb.debian.org/debian trixie/main arm64 libmaven-plugin-tools-java all 3.10.2-2 [245 kB] Get: 459 http://deb.debian.org/debian trixie/main arm64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 460 http://deb.debian.org/debian trixie/main arm64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 461 http://deb.debian.org/debian trixie/main arm64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 462 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.16-1 [19.2 kB] Get: 463 http://deb.debian.org/debian trixie/main arm64 libmuparserx4.0.12 arm64 4.0.12-2 [172 kB] Get: 464 http://deb.debian.org/debian trixie/main arm64 libmuparserx-dev arm64 4.0.12-2 [38.5 kB] Get: 465 http://deb.debian.org/debian trixie/main arm64 libpmix2t64 arm64 5.0.7-1 [585 kB] Get: 466 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.18.1+ds-2+b1 [1016 kB] Get: 467 http://deb.debian.org/debian trixie/main arm64 libopenmpi40 arm64 5.0.7-1 [2087 kB] Get: 468 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 5.0.7-1 [97.2 kB] Get: 469 http://deb.debian.org/debian trixie/main arm64 libpmix-dev arm64 5.0.7-1 [3947 kB] Get: 470 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 5.0.7-1 [180 kB] Get: 471 http://deb.debian.org/debian trixie/main arm64 libopenmpi-dev arm64 5.0.7-1 [1089 kB] Get: 472 http://deb.debian.org/debian trixie/main arm64 libprotobuf32t64 arm64 3.21.12-10+b6 [859 kB] Get: 473 http://deb.debian.org/debian trixie/main arm64 libprotobuf-lite32t64 arm64 3.21.12-10+b6 [250 kB] Get: 474 http://deb.debian.org/debian trixie/main arm64 libprotobuf-dev arm64 3.21.12-10+b6 [1263 kB] Get: 475 http://deb.debian.org/debian trixie/main arm64 libprotobuf-java all 3.21.12-10 [1268 kB] Get: 476 http://deb.debian.org/debian trixie/main arm64 libprotoc32t64 arm64 3.21.12-10+b6 [790 kB] Get: 477 http://deb.debian.org/debian trixie/main arm64 libspdlog1.15 arm64 1:1.15.2+ds-2 [99.1 kB] Get: 478 http://deb.debian.org/debian trixie/main arm64 libspdlog-dev arm64 1:1.15.2+ds-2 [91.1 kB] Get: 479 http://deb.debian.org/debian trixie/main arm64 libsurefire-java all 2.22.3-3 [1284 kB] Get: 480 http://deb.debian.org/debian trixie/main arm64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 481 http://deb.debian.org/debian trixie/main arm64 libwagon-http-java all 3.5.3-1 [49.5 kB] Get: 482 http://deb.debian.org/debian trixie/main arm64 libxml2-utils arm64 2.12.7+dfsg+really2.9.14-0.4 [98.3 kB] Get: 483 http://deb.debian.org/debian trixie/main arm64 maven all 3.9.9-1 [19.7 kB] Get: 484 http://deb.debian.org/debian trixie/main arm64 maven-repo-helper all 1.11 [142 kB] Get: 485 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-29 [163 kB] Get: 486 http://deb.debian.org/debian trixie/main arm64 maven-debian-helper all 2.6.7 [108 kB] Get: 487 http://deb.debian.org/debian trixie/main arm64 mpi-default-dev arm64 1.18 [3372 B] Get: 488 http://deb.debian.org/debian trixie/main arm64 protobuf-compiler arm64 3.21.12-10+b6 [84.9 kB] Get: 489 http://deb.debian.org/debian trixie/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 490 http://deb.debian.org/debian trixie/main arm64 testng all 6.9.12-4 [795 kB] Get: 491 http://deb.debian.org/debian trixie/main arm64 uuid-dev arm64 2.41-4 [49.5 kB] Fetched 368 MB in 1s (247 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19954 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.5-2_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package libapparmor1:arm64. Preparing to unpack .../libapparmor1_4.1.0-1_arm64.deb ... Unpacking libapparmor1:arm64 (4.1.0-1) ... Setting up libsystemd-shared:arm64 (257.5-2) ... Selecting previously unselected package systemd. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19967 files and directories currently installed.) Preparing to unpack .../systemd_257.5-2_arm64.deb ... Unpacking systemd (257.5-2) ... Setting up libapparmor1:arm64 (4.1.0-1) ... Setting up systemd (257.5-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20905 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.5-2_arm64.deb ... Unpacking systemd-sysv (257.5-2) ... Selecting previously unselected package libdbus-1-3:arm64. Preparing to unpack .../01-libdbus-1-3_1.16.2-2_arm64.deb ... Unpacking libdbus-1-3:arm64 (1.16.2-2) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../02-dbus-bin_1.16.2-2_arm64.deb ... Unpacking dbus-bin (1.16.2-2) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../03-dbus-session-bus-common_1.16.2-2_all.deb ... Unpacking dbus-session-bus-common (1.16.2-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../04-libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../05-dbus-daemon_1.16.2-2_arm64.deb ... Unpacking dbus-daemon (1.16.2-2) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../06-dbus-system-bus-common_1.16.2-2_all.deb ... Unpacking dbus-system-bus-common (1.16.2-2) ... Selecting previously unselected package dbus. Preparing to unpack .../07-dbus_1.16.2-2_arm64.deb ... Unpacking dbus (1.16.2-2) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../09-binfmt-support_2.2.2-7+b1_arm64.deb ... Unpacking binfmt-support (2.2.2-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../10-libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../11-python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21355 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-2_arm64.deb ... Unpacking python3-minimal (3.13.2-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... 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Setting up fontconfig-config (2.15.0-2.3) ... Setting up libmaven-parent-java (43-2) ... Setting up libevent-openssl-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-16) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:arm64 (2:1.3.4-1+b3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libsisu-inject-java (0.3.5-1) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up libnss3:arm64 (2:3.110-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1+b1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:arm64 (3.7.0-2) ... Setting up libxnvctrl0:arm64 (535.171.04-1+b2) ... Setting up libprotobuf-dev:arm64 (3.21.12-10+b6) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libltdl-dev:arm64 (2.5.4-4) ... Setting up libthai0:arm64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:arm64 (2.84.1-1) ... Setting up libmbedx509-7:arm64 (3.6.3-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:arm64 (1:17.0.6-21+b1) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libxfixes3:arm64 (1:6.0.0-2+b4) ... Setting up testng (6.9.12-4) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-2) ... Setting up dbus (1.16.2-2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libxinerama1:arm64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libxrandr2:arm64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libfmt-dev:arm64 (10.1.1+ds1-4) ... Setting up libspdlog1.15:arm64 (1:1.15.2+ds-2) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.8-2) ... Setting up libcommons-lang3-java (3.17.0-1) ... Setting up libevent-extra-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libmbedtls21:arm64 (3.6.3-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:arm64 (2.4.124-2) ... Setting up libnl-3-dev:arm64 (3.7.0-2) ... Setting up groff-base (1.23.0-7) ... Setting up libwayland-cursor0:arm64 (1.23.1-3) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-19) ... Setting up gpgconf (2.2.46-6) ... Setting up libpam-systemd:arm64 (257.5-2) ... Setting up libcommons-beanutils-java (1.9.4-2) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:arm64 (10.2.0-1+b1) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.12+dfsg-2) ... Setting up libhwloc-dev:arm64 (2.12.0-1) ... Setting up libsnappy-java (1.1.10.7-1) ... Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libfontconfig1:arm64 (2.15.0-2.3) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up gfortran-14 (14.2.0-19) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libavahi-client3:arm64 (0.8-16) ... Setting up libio-socket-ssl-perl (2.089-1) ... Setting up gpg (2.2.46-6) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libpython3-stdlib:arm64 (3.13.2-2) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.124-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up gtk-update-icon-cache (4.18.4+ds-1) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up mesa-libgallium:arm64 (25.0.3-1) ... Setting up velocity (1.7-7) ... Setting up libibverbs1:arm64 (56.1-1) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up gpg-agent (2.2.46-6) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libatk1.0-0t64:arm64 (2.56.1-2) ... Setting up openjdk-21-jre-headless:arm64 (21.0.7~8ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:arm64 (2:1.8.2-1) ... Setting up libgbm1:arm64 (25.0.3-1) ... Setting up ibverbs-providers:arm64 (56.1-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.3-2) ... Setting up libcommons-io-java (2.18.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up openssh-client (1:9.9p2-2) ... Setting up libxtst6:arm64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libxcursor1:arm64 (1:1.2.3-1) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libpango-1.0-0:arm64 (1.56.3-1) ... Setting up libgl1-mesa-dri:arm64 (25.0.3-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:arm64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:arm64 (0.3.6-2) ... Setting up python3 (3.13.2-2) ... Setting up sopv-gpgv (0.1.4-1) ... update-alternatives: using /usr/bin/sopv-gpgv to provide /usr/bin/sopv (sopv) in auto mode Setting up libhwloc-plugins:arm64 (2.12.0-1) ... Setting up libspdlog-dev:arm64 (1:1.15.2+ds-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:arm64 (1.18.4-1+b1) ... Setting up libcolord2:arm64 (1.4.7-3) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libdconf1:arm64 (0.40.0-5) ... Setting up libnl-route-3-dev:arm64 (3.7.0-2) ... Setting up libmaven-filtering-java (3.4.0-1) ... Setting up dbus-user-session (1.16.2-2) ... Setting up libmaven-resolver-java (1.9.22-1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up adwaita-icon-theme (48.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.017-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up libatspi2.0-0t64:arm64 (2.56.1-2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:arm64 (5.0.7-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up librdmacm1t64:arm64 (56.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libcairo-gobject2:arm64 (1.18.4-1+b1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:arm64 (2.4.10-2+b1) ... Setting up libpmix-dev:arm64 (5.0.7-1) ... Setting up libhsakmt1:arm64 (6.2.4+ds-1) ... Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libncbi-ngs3:arm64 (3.2.1+dfsg-3) ... Setting up libatk-bridge2.0-0t64:arm64 (2.56.1-2) ... Setting up libfabric1:arm64 (1.17.0-3.1) ... Setting up libngs-jni:arm64 (3.2.1+dfsg-3) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:arm64 (25.0.3-1) ... Setting up libglx0:arm64 (1.7.0-1+b2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:arm64 (8.13.0-1) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libcurlpp0t64:arm64 (0.8.1-6) ... Setting up debhelper (13.24.2) ... Setting up dconf-service (0.40.0-5) ... Setting up libibverbs-dev:arm64 (56.1-1) ... Setting up libgl1:arm64 (1.7.0-1+b2) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up cmake (3.31.6-2) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:arm64 (3.2.1+dfsg-3) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up libamdhip64-5 (5.7.1-5+b1) ... Setting up libcurl4-openssl-dev:arm64 (8.13.0-1) ... Setting up libcurlpp-dev:arm64 (0.8.1-6) ... Setting up libgtk-3-common (3.24.49-3) ... Setting up libucx0:arm64 (1.18.1+ds-2+b1) ... Setting up libgtk-3-0t64:arm64 (3.24.49-3) ... Setting up libopenmpi40:arm64 (5.0.7-1) ... Setting up openmpi-bin (5.0.7-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:arm64 (5.0.7-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up mpi-default-dev (1.18) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libwww-perl (6.78-1) ... Setting up devscripts (2.25.9) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.80) ... Setting up libprotobuf-java (3.21.12-10) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libguice-java (5.1.0-1) ... Setting up libplexus-i18n-java (1.0-beta-10-6) ... Setting up libplexus-container-default1.5-java (2.1.1-1) ... Setting up libplexus-velocity-java (1.2-4) ... Setting up libmaven3-core-java (3.9.9-1) ... Setting up libmaven-shared-incremental-java (1.1-6) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up libplexus-compiler-java (2.13.0-1) ... Setting up libmaven-compiler-plugin-java (3.13.0-1) ... Setting up libmaven-file-management-java (3.0.0-2) ... Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.13.0-1) ... Setting up libdoxia-core-java (2.0.0-1) ... Setting up libdoxia-java (2.0.0-1) ... Setting up libmaven-reporting-api-java (4.0.0-1) ... Setting up libmaven-reporting-exec-java (2.0.0-1) ... Processing triggers for libc-bin (2.41-7) ... Processing triggers for systemd (257.5-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven (3.9.9-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-21-jre:arm64 (21.0.7~8ea-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:arm64 (21.0.7~8ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up maven-repo-helper (1.11) ... Setting up default-jre (2:1.21-76) ... Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libplexus-ant-factory-java (1.0~alpha2.1-5) ... Setting up openjdk-21-jdk:arm64 (21.0.7~8ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up junit5 (5.10.3-1) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libmaven-plugin-tools-java (3.10.2-2) ... Setting up default-jdk (2:1.21-76) ... Setting up libsurefire-java (2.22.3-3) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-9) ... Setting up libdoxia-sitetools-java (2.0.0-1) ... Setting up libmaven-site-plugin-java (3.21.0-1) ... Setting up maven-debian-helper (2.6.7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/genomicsdb-1.5.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../genomicsdb_1.5.4-5_source.changes dpkg-buildpackage: info: source package genomicsdb dpkg-buildpackage: info: source version 1.5.4-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=cmake --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' # Removing the files we provided manually for the build of the component if [ -e genomicsdb-htslib/CMakeLists.txt ]; then rm genomicsdb-htslib/CMakeLists.txt; fi if [ -e genomicsdb-htslib/config.h ]; then rm genomicsdb-htslib/config.h; fi if [ -e genomicsdb-htslib/version.h ]; then rm genomicsdb-htslib/version.h; fi dh_auto_clean dh_auto_clean --buildsystem=maven bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgenomicsdb-java # Removing the debian/maven.properties file we setup during configure step. if [ -e debian/maven.properties ]; then rm debian/maven.properties; fi # Removing the patched pom.xml file. if [ -e pom.xml.old ]; then mv pom.xml.old pom.xml; fi make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' dh_autoreconf_clean -O--buildsystem=cmake jh_clean -O--buildsystem=cmake Duplicate specification "u=s" for option "u" dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake --with javahelper dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' # Preparing the build of the htslib component. cp debian/htslibComponentFiles/* genomicsdb-htslib/ echo '#define HTS_VERSION_TEXT ""' > genomicsdb-htslib/version.h # Configuring the C++ part using CMake. dh_auto_configure -- \ -DBUILD_JAVA:BOOL=False \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DJAVA_HOME:PATH=/usr/lib/jvm/default-java \ -DPROTOBUF_ROOT_DIR:PATH=/usr \ -DCMAKE_LIBRARY_ARCHITECTURE:STRING=aarch64-linux-gnu cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_JAVA:BOOL=False -DCMAKE_INSTALL_PREFIX:PATH=/usr -DJAVA_HOME:PATH=/usr/lib/jvm/default-java -DPROTOBUF_ROOT_DIR:PATH=/usr -DCMAKE_LIBRARY_ARCHITECTURE:STRING=aarch64-linux-gnu .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found BZip2: /usr/lib/aarch64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found CURL: /usr/lib/aarch64-linux-gnu/libcurl.so (found version "8.13.0") -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/aarch64-linux-gnu/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/aarch64-linux-gnu/liblzma.so - found -- Found LibLZMA: /usr/lib/aarch64-linux-gnu/liblzma.so (found version "5.8.1") CMake Deprecation Warning at genomicsdb-tiledb/CMakeLists.txt:29 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Found libuuid: /usr/include -- Found OpenSSL: /usr/lib/aarch64-linux-gnu/libcrypto.so (found version "3.5.0") -- Found CURL: /usr/lib/aarch64-linux-gnu/libcurl.so (found version "8.13.0") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- The TileDB library is compiled with verbosity. -- Found Catch2: /catch2/catch_all.hpp Version=3 -- GenomicsDB version=1.5.4 full_version=1.5.4-SNAPSHOT- -- CMAKE_BUILD_TYPE=None -- Performing Test test_cpp_2011 -- Performing Test test_cpp_2011 - Success -- Performing Test test_stack_protector_strong -- Performing Test test_stack_protector_strong - Success -- Found MPI_C: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Performing Test OPENMPV4_FOUND -- Performing Test OPENMPV4_FOUND - Success -- Performing Test STRING_VIEW_FOUND -- Performing Test STRING_VIEW_FOUND - Success -- string_view found -- RapidJSON found. Headers: /usr/include -- Found Spdlog: /usr/include -- Try finding Protobuf Library -- Could not find libcsv headers and/or libraries (missing: LIBCSV_LIBRARY LIBCSV_INCLUDE_DIR) -- Could not find safestring headers and/or libraries (missing: SAFESTRINGLIB_INCLUDE_DIR SAFESTRINGLIB_LIBRARY) CMake Warning (dev) at src/test/cpp/CMakeLists.txt:85 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/test/cpp/CMakeLists.txt:85 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (4.0s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' # Preparing the build of the htslib component. cp debian/htslibComponentFiles/* genomicsdb-htslib/ echo '#define HTS_VERSION_TEXT ""' > genomicsdb-htslib/version.h # Configuring the C++ part using CMake. dh_auto_configure -- \ -DBUILD_JAVA:BOOL=False \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DJAVA_HOME:PATH=/usr/lib/jvm/default-java \ -DPROTOBUF_ROOT_DIR:PATH=/usr \ -DCMAKE_LIBRARY_ARCHITECTURE:STRING=aarch64-linux-gnu cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_JAVA:BOOL=False -DCMAKE_INSTALL_PREFIX:PATH=/usr -DJAVA_HOME:PATH=/usr/lib/jvm/default-java -DPROTOBUF_ROOT_DIR:PATH=/usr -DCMAKE_LIBRARY_ARCHITECTURE:STRING=aarch64-linux-gnu .. -- Found CURL: /usr/lib/aarch64-linux-gnu/libcurl.so (found version "8.13.0") CMake Deprecation Warning at genomicsdb-tiledb/CMakeLists.txt:29 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found CURL: /usr/lib/aarch64-linux-gnu/libcurl.so (found version "8.13.0") -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- The TileDB library is compiled with verbosity. -- Found Catch2: /catch2/catch_all.hpp Version=3 -- GenomicsDB version=1.5.4 full_version=1.5.4-SNAPSHOT- -- CMAKE_BUILD_TYPE=None -- string_view found -- RapidJSON found. Headers: /usr/include -- Try finding Protobuf Library -- Could not find libcsv headers and/or libraries (missing: LIBCSV_LIBRARY LIBCSV_INCLUDE_DIR) -- Could not find safestring headers and/or libraries (missing: SAFESTRINGLIB_INCLUDE_DIR SAFESTRINGLIB_LIBRARY) CMake Warning (dev) at src/test/cpp/CMakeLists.txt:85 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/test/cpp/CMakeLists.txt:85 (add_custom_command): Exactly one of PRE_BUILD, PRE_LINK, or POST_BUILD must be given. Assuming POST_BUILD to preserve backward compatibility. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (0.8s) -- Generating done (0.3s) -- Build files have been written to: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu # Configuring the Java part using Maven. # First we put the arch triplet in d/maven.properties for the tests. echo "build.triplet=aarch64-linux-gnu" > debian/maven.properties mv pom.xml pom.xml.old sed 's/\${genomicsdb\.version}/1.5.4/; s,\${protoc\.filepath},/usr/bin/protoc,' pom.xml.old > pom.xml dh_auto_configure --buildsystem=maven skip faking of existing gnu-getopt:getopt::debian mh_patchpoms -plibgenomicsdb-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/genomicsdb-1.5.4/debian/maven-repo make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' jh_linkjars -O--buildsystem=cmake Duplicate specification "u=s" for option "u" debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/genomicsdb-1.5.4 -B/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/depend make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/depend make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/protobuf_ep.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 0%] Built target protobuf_ep [ 0%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -MF CMakeFiles/genomicsdb-hts.dir/kfunc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kfunc.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/kfunc.c [ 2%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o -MF CMakeFiles/genomicsdb-hts.dir/kstring.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kstring.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/kstring.c [ 2%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/resources /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake "--color=" [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array_iterator.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/knetfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/knetfile.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/knetfile.c [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o [ 3%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o [ 3%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o -MF CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o.d -o CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/bcf_sr_sort.c [ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o [ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o [ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array_schema.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o -MF CMakeFiles/genomicsdb-hts.dir/errmod.c.o.d -o CMakeFiles/genomicsdb-hts.dir/errmod.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/errmod.c cd 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-I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array_read_state.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o -MF CMakeFiles/genomicsdb-hts.dir/bgzf.c.o.d -o CMakeFiles/genomicsdb-hts.dir/bgzf.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/bgzf.c cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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[ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o -MF CMakeFiles/genomicsdb-hts.dir/header.c.o.d -o CMakeFiles/genomicsdb-hts.dir/header.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/header.c [ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile.c [ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile_libcurl.c [ 5%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array_sorted_read_state.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 5%] Built target PROTOBUF_GENERATED_CXX_TARGET make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile_libcurl.c: In function 'libcurl_open': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile_libcurl.c:47: /usr/include/aarch64-linux-gnu/curl/curl.h:2932:3: note: declared here 2932 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations.cc [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hts.c [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hfile_net.c [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts_os.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/hts_os.c [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o -MF CMakeFiles/genomicsdb-hts.dir/md5.c.o.d -o CMakeFiles/genomicsdb-hts.dir/md5.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/md5.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o -MF CMakeFiles/genomicsdb-hts.dir/multipart.c.o.d -o CMakeFiles/genomicsdb-hts.dir/multipart.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/multipart.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o -MF CMakeFiles/genomicsdb-hts.dir/probaln.c.o.d -o CMakeFiles/genomicsdb-hts.dir/probaln.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/probaln.c [ 7%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o -MF CMakeFiles/genomicsdb-hts.dir/realn.c.o.d -o CMakeFiles/genomicsdb-hts.dir/realn.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/realn.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o -MF CMakeFiles/genomicsdb-hts.dir/regidx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/regidx.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/regidx.c [ 7%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations_columnar.cc [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o -MF CMakeFiles/genomicsdb-hts.dir/region.c.o.d -o CMakeFiles/genomicsdb-hts.dir/region.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/region.c [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o -MF CMakeFiles/genomicsdb-hts.dir/sam.c.o.d -o CMakeFiles/genomicsdb-hts.dir/sam.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/sam.c [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o -MF CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o.d -o CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/synced_bcf_reader.c [ 8%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/array/array_sorted_write_state.cc [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/vcf_sweep.c In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o -MF CMakeFiles/genomicsdb-hts.dir/tbx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/tbx.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/tbx.c In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations_columnar.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/textutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/textutils.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/textutils.c [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o -MF CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o.d -o CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/thread_pool.c [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcf.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcf.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/vcf.c [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -MF CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o.d -o CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/vcfutils.c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations.cc: In member function 'virtual void AlleleCountOperator::operate_on_columnar_cell(const GenomicsDBColumnarCell&, const VariantQueryConfig&, const VariantArraySchema&)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations.cc:984:36: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 984 | auto REF_ALT_pair = std::move(std::pair( | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 985 | std::string(REF_ptr, REF_length), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 986 | std::string(ALT_ptr+m_cell_ALT_offsets[ALT_idx], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 987 | m_cell_ALT_offsets[ALT_idx+1]-m_cell_ALT_offsets[ALT_idx]-1))); //-1 to ignore delim char | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/variant_operations.cc:984:36: note: remove 'std::move' call [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_codecs.c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc: In member function 'void BroadCombinedGVCFOperator::handle_INFO_fields(const Variant&)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:622:37: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 622 | auto stringified = std::move(m_field_handlers[bcf_ht_type]->stringify_2D_vector(*(BCF_INFO_GET_FIELD_INFO_PTR(curr_tuple)))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:622:37: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:643:34: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 643 | auto result_str = std::move( | ~~~~~~~~~^ 644 | GET_HISTOGRAM_FIELD_HANDLER_PTR_FROM_TUPLE(curr_INFO_histogram_tuple)->stringify_histogram( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 645 | length_descriptor.get_vcf_delimiter(0u), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 646 | length_descriptor.get_vcf_delimiter(1u) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 647 | )); | ~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:643:34: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc: In member function 'void BroadCombinedGVCFOperator::handle_deletions(Variant&)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:1106:37: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 1106 | auto null_PL_ptr = std::move(std::unique_ptr(nullptr)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:1106:37: note: remove 'std::move' call [ 11%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_decode.c [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_encode.c [ 12%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc [ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_external.c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc: In function 'int tiledb_array_set_schema(TileDB_ArraySchema*, const char*, const char**, int, int64_t, int, const int*, const int*, const int*, const int*, const int*, int, const char**, int, const void*, size_t, const void*, size_t, int, const int*)': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:409:22: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 409 | (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/cstdlib:79, from /usr/include/c++/14/ext/string_conversions.h:43, from /usr/include/c++/14/bits/basic_string.h:4154, from /usr/include/c++/14/string:54, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api/tiledb.h:44, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:36: /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:440:62: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 440 | tiledb_array_schema->offsets_compression_ = (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:440:62: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 440 | tiledb_array_schema->offsets_compression_ = (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:448:68: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 448 | tiledb_array_schema->offsets_compression_level_ = (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:448:68: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 448 | tiledb_array_schema->offsets_compression_level_ = (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:440:62: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 440 | tiledb_array_schema->offsets_compression_ = (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ [ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_index.c [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec.cc /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc: In function 'int tiledb_metadata_set_schema(TileDB_MetadataSchema*, const char*, const char**, int, int64_t, const int*, const int*, const int*, const int*)': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc:1131:22: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1131 | (int*) malloc((attribute_num)*sizeof(int)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function 'void* malloc(size_t)' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ [ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_io.c [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_blosc.cc [ 14%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_filter.cc [ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_samtools.c [ 14%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_filter_bit_shuffle.cc [ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/cram_stats.c [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc [ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/mFILE.c [ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/open_trace_file.c [ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_gzip.cc [ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/pooled_alloc.c [ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/rANS_static.c [ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib/cram/string_alloc.c [ 18%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc [ 18%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc [ 18%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_lz4.cc [ 18%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_cell.cc [ 19%] Linking C shared library libgenomicsdb-hts.so cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb-hts.dir/link.txt --verbose=1 [ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_rle.cc /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/genomicsdb-hts.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-hts.so -o libgenomicsdb-hts.so "CMakeFiles/genomicsdb-hts.dir/kfunc.c.o" "CMakeFiles/genomicsdb-hts.dir/knetfile.c.o" "CMakeFiles/genomicsdb-hts.dir/kstring.c.o" "CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o" "CMakeFiles/genomicsdb-hts.dir/bgzf.c.o" "CMakeFiles/genomicsdb-hts.dir/errmod.c.o" "CMakeFiles/genomicsdb-hts.dir/faidx.c.o" "CMakeFiles/genomicsdb-hts.dir/header.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o" "CMakeFiles/genomicsdb-hts.dir/hts.c.o" "CMakeFiles/genomicsdb-hts.dir/hts_os.c.o" "CMakeFiles/genomicsdb-hts.dir/md5.c.o" "CMakeFiles/genomicsdb-hts.dir/multipart.c.o" "CMakeFiles/genomicsdb-hts.dir/probaln.c.o" "CMakeFiles/genomicsdb-hts.dir/realn.c.o" "CMakeFiles/genomicsdb-hts.dir/regidx.c.o" "CMakeFiles/genomicsdb-hts.dir/region.c.o" "CMakeFiles/genomicsdb-hts.dir/sam.c.o" "CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o" "CMakeFiles/genomicsdb-hts.dir/tbx.c.o" "CMakeFiles/genomicsdb-hts.dir/textutils.c.o" "CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf.c.o" "CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o" /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/liblzma.so make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 19%] Built target genomicsdb-hts [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/codec_zstd.cc [ 20%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/bitshuffle_core.c [ 20%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/iochain.c [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/expressions/expression.cc [ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/fragment/book_keeping.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_cell.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/fragment/fragment.cc [ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/fragment/read_state.cc [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/fragment/write_state.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/gt_remapper.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/gt_remapper_template_definition.h:25, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:28: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/metadata/metadata.cc [ 23%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_field_data.cc [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/metadata/metadata_iterator.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_field_data.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_construct.h:61, from /usr/include/c++/14/bits/stl_tempbuf.h:61, from /usr/include/c++/14/memory:66, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc [ 24%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/error.cc [ 24%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/hilbert_curve.cc [ 24%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/mem_utils.cc [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/progress_bar.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_array_schema.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/uri.cc [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/misc/utils.cc [ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc [ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/storage/storage_buffer.cc [ 27%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/storage/storage_fs.cc [ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/query_variants.cc [ 27%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/storage/storage_manager.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/variant.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/storage/storage_manager_config.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/query_variants.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/query_variants.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/storage/storage_posixfs.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/src/codec/external/lz4/lz4.c [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/load_operators.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/genomicsdb_importer.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader_file_base.cc [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/load_operators.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/memory_measure.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc:32: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader_file_base.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader_text_file.h:33, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc:30: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 31%] Built target TILEDB_CORE_OBJECTS make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 31%] Linking CXX static library libgenomicsdb-tiledb.a [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -P CMakeFiles/tiledb_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/histogram.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_static.dir/link.txt --verbose=1 In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/genomicsdb_importer.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:27: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/ar qc libgenomicsdb-tiledb.a CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o /usr/bin/ranlib libgenomicsdb-tiledb.a make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 31%] Built target tiledb_static make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc: In member function 'std::vector GenomicsDBMultiDVectorField::parse_and_store_numeric(const char*, size_t)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:436:50: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 436 | auto total_size_of_multi_d_data_vec = std::move(GenomicsDBMultiDVectorField::parse_and_store_numeric( | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 | m_rw_field_data, *m_field_info_ptr, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 | str, str_length)); | ~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:436:50: note: remove 'std::move' call [ 32%] Linking CXX shared library libgenomicsdb-tiledb.so cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_shared.dir/link.txt --verbose=1 In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader.cc:27: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, from /usr/include/fmt/format.h:36, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/loader/tiledb_loader.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,--dependency-file=CMakeFiles/tiledb_shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-tiledb.so -o libgenomicsdb-tiledb.so CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 32%] Built target tiledb_shared make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 32%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -MF CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d -o CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/array/test_array_schema.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper_pb.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/lut.cc [ 33%] Linking CXX executable test_array_schema cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_array_schema.dir/link.d CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o -o test_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 33%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 33%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -MF CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d -o CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/benchmark/test_print_array_schema.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/known_field_info.cc [ 34%] Linking CXX executable test_print_array_schema cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_array_schema.dir/link.txt --verbose=1 [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_print_array_schema.dir/link.d CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -o test_print_array_schema ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 35%] Built target test_print_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 35%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -MF CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o.d -o CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/benchmark/test_print_book_keeping.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/known_field_info.cc:27: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/known_field_info.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/known_field_info.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Linking CXX executable test_print_book_keeping cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_book_keeping.dir/link.txt --verbose=1 In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:33: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper_sql.cc [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/timer.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_print_book_keeping.dir/link.d CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o -o test_print_book_keeping ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 35%] Built target test_print_book_keeping make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/genomicsdb_logger.cc [ 35%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -MF CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o.d -o CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc: In member function 'void VidMapper::parse_string_length_descriptor(const char*, const char*, size_t, FieldLengthDescriptor&, size_t)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:757:47: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 757 | auto length_value_upper_case_str = std::move(std::string(length_value_str)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:757:47: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc: In member function 'void FileBasedVidMapper::common_constructor_initialization(const rapidjson::Value&)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:1269:40: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 1269 | auto class_name = std::move(std::string(vcf_field_class_array[i].GetString())); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/vid_mapper.cc:1269:40: note: remove 'std::move' call [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/vcf_adapter.cc [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/vcf2binary.cc [ 37%] Building C object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cc -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/hfile_genomicsdb.c [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/alleles_combiner.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/alleles_combiner_template_definition.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc:23: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/vcf2binary.cc:29: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/vcf/vcf2binary.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/variant_query_config.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/genomicsdb_config_base.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/genomicsdb_config_base.cc: In member function 'const bool GenomicsDBConfigBase::has_array_name(int) const': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/genomicsdb_config_base.cc:101:53: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'const int' [-Wsign-compare] 101 | (!m_single_array_name && m_array_names.size() > rank)) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/variant_query_config.cc:26: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/variant_query_config.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc: In member function 'rapidjson::Document GenomicsDBConfigBase::read_from_file(const std::string&, int)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc:193:43: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 193 | rapidjson::Document json_doc = std::move(parse_json_file(filename)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc:193:43: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc: In member function 'void GenomicsDBImportConfig::read_from_file(const std::string&, int)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc:704:43: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 704 | rapidjson::Document json_doc = std::move(GenomicsDBConfigBase::read_from_file(filename, rank)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/config/json_config.cc:704:43: note: remove 'std::move' call [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 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-I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/annotation_service.cc [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_field.cc [ 41%] Linking CXX executable test_sparse_array_benchmark cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_benchmark.dir/link.txt --verbose=1 [ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_plink.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_sparse_array_benchmark.dir/link.d CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o -o test_sparse_array_benchmark ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc:46: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api/genomicsdb.h:37, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc:34: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Built target test_sparse_array_benchmark make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 41%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -MF CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o.d -o CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc [ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_utils.cc [ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_json_processor.cc [ 42%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/genomicsdb_coordinates.pb.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_plink.cc:40: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api/genomicsdb.h:37, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api/genomicsdb_plink.h:35, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb_plink.cc:34: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/genomicsdb_callsets_mapping.pb.cc [ 42%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/genomicsdb_export_config.pb.cc [ 43%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/genomicsdb_import_config.pb.cc [ 43%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/genomicsdb_vid_mapping.pb.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o -MF CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o.d -o CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -MF CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o.d -o CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/c_api/test_dense_array_api.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o -MF CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o.d -o CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/c_api/test_sparse_array_api.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o -MF CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o.d -o CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/c_api/test_tiledb_utils.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake "--color=" [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o -MF CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o.d -o CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/codec/test_codec.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build In file included from /usr/include/c++/14/bits/basic_string.h:47, from /usr/include/c++/14/string:54: In function 'constexpr std::size_t std::__sv_check(size_t, size_t, const char*)', inlined from 'constexpr std::basic_string_view<_CharT, _Traits> std::basic_string_view<_CharT, _Traits>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits]' at /usr/include/c++/14/string_view:336:25, inlined from 'std::string_view get_segment(std::string_view, int)' at /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc:820:20: /usr/include/c++/14/string_view:72:5: warning: 'pos' may be used uninitialized [-Wmaybe-uninitialized] 72 | if (__pos > __size) | ^~ /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc: In function 'std::string_view get_segment(std::string_view, int)': /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/src/api/genomicsdb.cc:807:26: note: 'pos' was declared here 807 | std::string::size_type pos; | ^~~ make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o -MF CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o.d -o CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/codec/test_codec_filter.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o -MF CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o.d -o CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/expressions/test_expressions.cc [ 46%] Linking CXX executable test_array_iterator cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_iterator.dir/link.txt --verbose=1 make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 47%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o -MF CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o.d -o CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/expressions/test_filter_api.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_array_iterator.dir/link.d CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o -o test_array_iterator ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 47%] Built target test_array_iterator make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 47%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -MF CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d -o CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_mem_utils.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f 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-I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o -MF CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o.d -o CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_uri.cc [ 48%] Linking CXX executable test_codec cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec.dir/link.txt --verbose=1 [ 48%] Linking CXX executable test_codec_filter cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_codec.dir/link.d CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o -o test_codec ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 48%] Built target test_codec make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 49%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -MF CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o.d -o CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_codec_filter.dir/link.d CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o -o test_codec_filter ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 49%] Built target test_codec_filter make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/../core/include/expressions 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'/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 50%] Built target test_mem_utils make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f 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-std=c++17 -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -MF CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o.d -o CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc [ 50%] Linking CXX executable test_filter_api cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_filter_api.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_filter_api.dir/link.d CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o -o test_filter_api ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 50%] Built target test_filter_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o -MF CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o.d -o CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_3d.cc make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o -MF CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o.d -o CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_aio_read_dense.cc [ 51%] Linking CXX executable tiledb_array_3d cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_3d.dir/link.txt --verbose=1 [ 51%] Linking CXX executable test_uri cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_uri.dir/link.txt --verbose=1 [ 51%] Linking CXX executable tiledb_array_aio_read_dense cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_aio_read_dense.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_3d.dir/link.d CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o -o tiledb_array_3d ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_uri.dir/link.d CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o -o test_uri ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 51%] Built target tiledb_array_3d make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake "--color=" [ 51%] Built target test_uri make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 52%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o -MF CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o.d -o CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_aio_write_dense.cc [ 52%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -MF CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d -o CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_consolidate.cc [ 52%] Linking CXX executable test_array_schema_api cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema_api.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_aio_read_dense.dir/link.d CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o -o tiledb_array_aio_read_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 52%] Built target tiledb_array_aio_read_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 52%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -MF CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o.d -o CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_create_dense.cc [ 52%] Linking CXX executable tiledb_array_aio_write_dense cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_aio_write_dense.dir/link.txt --verbose=1 [ 53%] Linking CXX executable tiledb_array_consolidate cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_consolidate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_array_schema_api.dir/link.d CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o -o test_array_schema_api ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 53%] Built target test_array_schema_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build [ 53%] Linking CXX executable tiledb_array_create_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_dense.dir/link.txt --verbose=1 [ 53%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o -MF CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o.d -o CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_create_sparse.cc [ 54%] Linking CXX executable test_dense_array_api cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_dense_array_api.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_aio_write_dense.dir/link.d CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o -o tiledb_array_aio_write_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 54%] Built target tiledb_array_aio_write_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_consolidate.dir/link.d CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o -o tiledb_array_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 54%] Built target tiledb_array_consolidate make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 54%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -MF CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o.d -o CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_dense.cc [ 55%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o -MF CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o.d -o CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 55%] Built target GenomicsDB_library_object_files make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 56%] Linking CXX executable tiledb_array_create_sparse cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_sparse.dir/link.txt --verbose=1 [ 56%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o -MF CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o.d -o CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse_filter.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_create_dense.dir/link.d CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o -o tiledb_array_create_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_dense_array_api.dir/link.d CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o -o test_dense_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' In file included from /usr/include/string.h:548, from /usr/include/c++/14/cstring:43, from /usr/include/catch2/internal/catch_stringref.hpp:16, from /usr/include/catch2/interfaces/catch_interfaces_capture.hpp:13, from /usr/include/catch2/benchmark/catch_benchmark.hpp:19, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/include/catch2/catch.h:39, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:39: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:184:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:10: note: source object 'j' of size 8 181 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:186:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:19: note: source object 'k' of size 8 181 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:191:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:10: note: source object 'j' of size 8 181 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:192:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:19: note: source object 'k' of size 8 181 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:196:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:10: note: source object 'j' of size 8 181 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:198:11: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:29:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading 16 bytes from a region of size 8 [-Wstringop-overread] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:181:19: note: source object 'k' of size 8 181 | double j = 0.1, k = 0.2; | ^ [ 56%] Built target tiledb_array_create_dense [ 56%] Built target test_dense_array_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 56%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o -MF CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o.d -o CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_dense.cc make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build [ 56%] Linking CXX executable tiledb_array_iterator_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_dense.dir/link.txt --verbose=1 [ 56%] Linking CXX executable tiledb_array_iterator_sparse cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse.dir/link.txt --verbose=1 [ 57%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -MF CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d -o CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_sparse.cc [ 58%] Linking CXX executable tiledb_array_iterator_sparse_filter cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_create_sparse.dir/link.d CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o -o tiledb_array_create_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 58%] Built target tiledb_array_create_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 58%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -MF CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_1.cc [ 58%] Linking CXX executable tiledb_array_parallel_consolidate_dense cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_iterator_sparse.dir/link.d CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o -o tiledb_array_iterator_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 58%] Built target tiledb_array_iterator_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake "--color=" [ 58%] Linking CXX executable tiledb_array_parallel_consolidate_sparse make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 59%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -MF CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_2.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_iterator_dense.dir/link.d CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o -o tiledb_array_iterator_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 59%] Linking CXX executable tiledb_array_parallel_read_dense_1 [ 59%] Built target tiledb_array_iterator_dense cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_dense_1.dir/link.txt --verbose=1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_iterator_sparse_filter.dir/link.d CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o -o tiledb_array_iterator_sparse_filter ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 59%] Built target tiledb_array_iterator_sparse_filter make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake "--color=" [ 59%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -MF CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_mpi_io_dense.cc [ 59%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -MF CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_1.cc [ 59%] Linking CXX executable tiledb_array_parallel_read_dense_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_dense_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/link.d CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o -o tiledb_array_parallel_consolidate_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.d CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o -o tiledb_array_parallel_consolidate_sparse ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx [ 59%] Built target tiledb_array_parallel_consolidate_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake "--color=" [ 59%] Built target tiledb_array_parallel_consolidate_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_read_dense_1.dir/link.d CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o -o tiledb_array_parallel_read_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx [ 60%] Linking CXX executable tiledb_array_parallel_read_mpi_io_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/link.txt --verbose=1 [ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o [ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -MF CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_1.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -MF CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_2.cc [ 61%] Built target tiledb_array_parallel_read_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 61%] Linking CXX executable tiledb_array_parallel_read_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.txt --verbose=1 [ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -MF CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_2.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/link.d CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o -o tiledb_array_parallel_read_mpi_io_dense ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 61%] Built target tiledb_array_parallel_read_mpi_io_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -MF CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_1.cc [ 62%] Linking CXX executable tiledb_array_parallel_write_dense_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_read_dense_2.dir/link.d CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o -o tiledb_array_parallel_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx [ 62%] Linking CXX executable tiledb_array_parallel_write_dense_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.txt --verbose=1 [ 62%] Built target tiledb_array_parallel_read_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake "--color=" [ 62%] Linking CXX executable tiledb_array_parallel_read_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -MF CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_2.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.d CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o -o tiledb_array_parallel_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 62%] Built target tiledb_array_parallel_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 63%] Linking CXX executable tiledb_array_parallel_write_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.txt --verbose=1 [ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -MF CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d -o CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_primitive.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_write_dense_1.dir/link.d CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o -o tiledb_array_parallel_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 64%] Built target tiledb_array_parallel_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/link.d CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o -o tiledb_array_parallel_read_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake "--color=" [ 64%] Built target tiledb_array_parallel_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -MF CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o.d -o CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_1.cc [ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -MF CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d -o CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_2.cc [ 64%] Linking CXX executable tiledb_array_parallel_write_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.d CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o -o tiledb_array_parallel_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 64%] Built target tiledb_array_parallel_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -MF CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d -o CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_3.cc [ 66%] Linking CXX executable test_tiledb_utils cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tiledb_utils.dir/link.txt --verbose=1 [ 66%] Linking CXX executable tiledb_array_primitive cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_primitive.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.d CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o -o tiledb_array_parallel_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 66%] Built target tiledb_array_parallel_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 66%] Linking CXX executable tiledb_array_read_dense_2 [ 66%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -MF CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o.d -o CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_sorted.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/link.d CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o -o tiledb_array_parallel_write_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 67%] Linking CXX executable tiledb_array_read_dense_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_1.dir/link.txt --verbose=1 [ 67%] Built target tiledb_array_parallel_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -MF CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_1.cc [ 67%] Linking CXX executable tiledb_array_read_dense_3 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_primitive.dir/link.d CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o -o tiledb_array_primitive ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 67%] Built target tiledb_array_primitive make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_dense_2.dir/link.d CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o -o tiledb_array_read_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_tiledb_utils.dir/link.d CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o -o test_tiledb_utils ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 68%] Linking CXX executable tiledb_array_read_dense_sorted cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_sorted.dir/link.txt --verbose=1 [ 68%] Built target tiledb_array_read_dense_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build [ 68%] Linking CXX executable tiledb_array_read_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_1.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend [ 68%] Built target test_tiledb_utils make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake "--color=" [ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -MF CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -MF CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_1.cc [ 69%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -MF CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_2.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_dense_1.dir/link.d CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o -o tiledb_array_read_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 69%] Built target tiledb_array_read_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 69%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -MF CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o.d -o CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_sorted.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_dense_3.dir/link.d CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o -o tiledb_array_read_dense_3 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 69%] Built target tiledb_array_read_dense_3 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake "--color=" [ 70%] Linking CXX executable tiledb_array_read_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 70%] Linking CXX executable tiledb_array_read_sparse_filter_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_1.dir/link.txt --verbose=1 [ 70%] Linking CXX executable tiledb_array_read_sparse_filter_2 [ 70%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -MF CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o.d -o CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_1.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_sparse_1.dir/link.d CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o -o tiledb_array_read_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_dense_sorted.dir/link.d CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o -o tiledb_array_read_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 70%] Built target tiledb_array_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend [ 70%] Built target tiledb_array_read_dense_sorted make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -MF CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o.d -o CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_2.cc [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -MF CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_1.cc [ 72%] Linking CXX executable tiledb_array_read_sparse_sorted cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.txt --verbose=1 [ 72%] Linking CXX executable tiledb_array_update_dense_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.d CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o -o tiledb_array_read_sparse_filter_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_sparse_2.dir/link.d CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o -o tiledb_array_read_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 72%] Linking CXX executable tiledb_array_update_dense_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_2.dir/link.txt --verbose=1 [ 72%] Built target tiledb_array_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake "--color=" [ 72%] Built target tiledb_array_read_sparse_filter_2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_sparse_filter_1.dir/link.d CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o -o tiledb_array_read_sparse_filter_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake "--color=" [ 72%] Built target tiledb_array_read_sparse_filter_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake "--color=" [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -MF CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -MF CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o.d -o CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_2.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -MF CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o.d -o CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc [ 73%] Linking CXX executable tiledb_array_update_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.d CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o -o tiledb_array_read_sparse_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 73%] Built target tiledb_array_read_sparse_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_update_dense_1.dir/link.d CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o -o tiledb_array_update_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 73%] Built target tiledb_array_update_dense_1 [ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -MF CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d -o CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_sorted.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -MF CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_1.cc [ 75%] Linking CXX executable tiledb_array_write_dense_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_1.dir/link.txt --verbose=1 [ 75%] Linking CXX executable tiledb_array_update_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_update_dense_2.dir/link.d CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o -o tiledb_array_update_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 75%] Linking CXX executable tiledb_array_write_dense_2 [ 75%] Built target tiledb_array_update_dense_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_2.dir/link.txt --verbose=1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_update_sparse_1.dir/link.d CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -o tiledb_array_update_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 75%] Built target tiledb_array_update_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend [ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -MF CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 75%] Linking CXX executable tiledb_array_write_dense_sorted cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_sorted.dir/link.txt --verbose=1 [ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -MF CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_3.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_update_sparse_2.dir/link.d CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o -o tiledb_array_update_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 75%] Built target tiledb_array_update_sparse_2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_dense_2.dir/link.d CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -o tiledb_array_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake "--color=" [ 75%] Built target tiledb_array_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend [ 76%] Linking CXX executable tiledb_array_write_sparse_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 77%] Linking CXX executable tiledb_array_write_sparse_3 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_3.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_dense_1.dir/link.d CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o -o tiledb_array_write_dense_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -MF CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o.d -o CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_4.cc [ 77%] Built target tiledb_array_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake "--color=" [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -MF CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d -o CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_catching_errors.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -MF CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d -o CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_clear_delete_move.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_dense_sorted.dir/link.d CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o -o tiledb_array_write_dense_sorted ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 78%] Linking CXX executable tiledb_array_write_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_2.dir/link.txt --verbose=1 [ 78%] Built target tiledb_array_write_dense_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -MF CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d -o CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_config.cc [ 78%] Linking CXX executable tiledb_catching_errors cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_catching_errors.dir/link.txt --verbose=1 [ 78%] Linking CXX executable tiledb_array_write_sparse_4 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_4.dir/link.txt --verbose=1 [ 79%] Linking CXX executable tiledb_clear_delete_move cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_clear_delete_move.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_sparse_1.dir/link.d CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o -o tiledb_array_write_sparse_1 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 79%] Linking CXX executable tiledb_config [ 79%] Built target tiledb_array_write_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_config.dir/link.txt --verbose=1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_sparse_3.dir/link.d CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o -o tiledb_array_write_sparse_3 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 79%] Built target tiledb_array_write_sparse_3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_catching_errors.dir/link.d CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o -o tiledb_catching_errors ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx [ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -MF CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d -o CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_delete.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake "--color=" [ 80%] Built target tiledb_catching_errors make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_sparse_2.dir/link.d CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o -o tiledb_array_write_sparse_2 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 80%] Built target tiledb_array_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend [ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -MF CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d -o CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_ls_workspaces.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake "--color=" [ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -MF CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d -o CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_ls.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -MF CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d -o CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_consolidate.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_clear_delete_move.dir/link.d CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o -o tiledb_clear_delete_move ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_array_write_sparse_4.dir/link.d CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o -o tiledb_array_write_sparse_4 ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 80%] Built target tiledb_clear_delete_move make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake "--color=" [ 80%] Built target tiledb_array_write_sparse_4 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build [ 80%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -MF CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d -o CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_create.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_config.dir/link.d CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o -o tiledb_config ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 81%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -MF CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d -o CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_iterator.cc [ 81%] Built target tiledb_config make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake "--color=" [ 81%] Linking CXX executable tiledb_ls_workspaces make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls_workspaces.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 82%] Linking CXX executable tiledb_ls cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls.dir/link.txt --verbose=1 [ 82%] Linking CXX executable tiledb_delete [ 82%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -MF CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d -o CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_primitive.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_delete.dir/link.txt --verbose=1 [ 83%] Linking CXX executable tiledb_metadata_consolidate cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_consolidate.dir/link.txt --verbose=1 [ 83%] Linking CXX executable test_storage_buffer cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_storage_buffer.dir/link.txt --verbose=1 [ 83%] Linking CXX executable tiledb_metadata_create cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_create.dir/link.txt --verbose=1 [ 83%] Linking CXX executable tiledb_metadata_iterator cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_iterator.dir/link.txt --verbose=1 [ 84%] Linking CXX executable tiledb_metadata_primitive cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_primitive.dir/link.txt --verbose=1 [ 84%] Linking CXX executable test_utils cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_utils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_ls_workspaces.dir/link.d CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o -o tiledb_ls_workspaces ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 84%] Built target tiledb_ls_workspaces /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_ls.dir/link.d CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o -o tiledb_ls ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_delete.dir/link.d CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o -o tiledb_delete ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx [ 84%] Built target tiledb_ls make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build [ 84%] Built target tiledb_delete /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_consolidate.dir/link.d CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o -o tiledb_metadata_consolidate ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 84%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -MF CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d -o CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_read.cc [ 85%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -MF CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d -o CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_update.cc make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend [ 85%] Built target tiledb_metadata_consolidate make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_storage_buffer.dir/link.d CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o -o test_storage_buffer ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 85%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -MF CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o.d -o CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_workspace_group_create.cc [ 85%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -std=c++17 -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -MF CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o.d -o CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/src/tiledb_metadata_write.cc [ 85%] Built target test_storage_buffer make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_create.dir/link.d CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o -o tiledb_metadata_create ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_iterator.dir/link.d CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o -o tiledb_metadata_iterator ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 85%] Built target tiledb_metadata_create make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 85%] Built target tiledb_metadata_iterator make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake "--color=" [ 85%] Linking CXX shared library libgenomicsdb.so cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledbgenomicsdb.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas 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CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o CMakeFiles/GenomicsDBmake[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 85%] Linking CXX static library libgenomicsdb.a cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cmake -P CMakeFiles/genomicsdb.dir/cmake_clean_target.cmake cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_primitive.dir/link.d CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o -o tiledb_metadata_primitive ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so 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CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets[ 85%] Built target tiledb_metadata_primitive [ 85%] Linking CXX executable tiledb_metadata_read cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_read.dir/link.txt --verbose=1 [ 85%] Linking CXX executable tiledb_metadata_update cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_update.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target tiledb_metadata_update /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_read.dir/link.d CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -o tiledb_metadata_read ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target tiledb_metadata_read /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_metadata_write.dir/link.d CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o -o tiledb_metadata_write ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target tiledb_metadata_write /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tiledb_workspace_group_create.dir/link.d CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o -o tiledb_workspace_group_create ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target tiledb_workspace_group_create _mapping.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o /usr/bin/ranlib libgenomicsdb.a make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target genomicsdb make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/depend make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend make -f 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/usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -MF CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d -o CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/tools/src/consolidate_genomicsdb_array.cc [ 88%] Building CXX object tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -MF CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o.d -o CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/tools/src/gt_mpi_gather.cc _library_object_files.dir/cpp/src/api/genomicsdb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o -Wl,-rpath,/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core: /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/liblzma.so cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cmake -E cmake_symlink_library libgenomicsdb.so.1.5.4 libgenomicsdb.so.1 libgenomicsdb.so make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 88%] Built target tiledbgenomicsdb make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 88%] Building CXX object tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -MF CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d -o CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc [ 88%] Linking CXX executable test_posixfs cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_posixfs.dir/link.txt --verbose=1 In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/gt_mpi_gather.cc:30: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/gt_mpi_gather.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_posixfs.dir/link.d CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -o test_posixfs ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 88%] Built target test_posixfs make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 89%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -MF CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d -o CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf_histogram.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf2genomicsdb.cc:26: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/bits/hashtable_policy.h:36, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /usr/include/c++/14/functional:63, from /usr/include/spdlog/common.h:13, from /usr/include/spdlog/spdlog.h:12, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/genomicsdb_logger.h:41, from /build/reproducible-path/genomicsdb-1.5.4/tools/include/common.h:27, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf2genomicsdb.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/tools/include/vcfdiff.h:31, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/tools/include/vcfdiff.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/consolidate_genomicsdb_array.cc:29: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/consolidate_genomicsdb_array.cc:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o -MF CMakeFiles/ctests.dir/src/test_config.cc.o.d -o CMakeFiles/ctests.dir/src/test_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_config.cc [ 90%] Building CXX object src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -MF CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d -o CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_genomicsdb_api.cc /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf2genomicsdb.cc: In function 'int main(int, char**)': /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf2genomicsdb.cc:165:45: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 165 | auto loader_json_config_file = std::move(std::string(argv[optind])); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf2genomicsdb.cc:165:45: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc: In constructor 'VCFDiffFile::VCFDiffFile(const std::string&, const std::string&)': /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:83:41: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 83 | std::string field_name = std::move(std::string(bcf_hdr_int2id(m_hdr, BCF_DT_ID, i))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:83:41: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc: In member function 'void VCFDiffFile::compare_line(const bcf_hdr_t*, bcf1_t*)': /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:591:33: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 591 | auto gold_ID_set = std::move(get_ID_set(gold_line)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:591:33: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:592:33: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 592 | auto test_ID_set = std::move(get_ID_set(m_line)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcfdiff.cc:592:33: note: remove 'std::move' call [ 90%] Linking CXX executable test_sparse_array_api cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_api.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_sparse_array_api.dir/link.d CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o -o test_sparse_array_api ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 90%] Built target test_sparse_array_api make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf_histogram.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.4/tools/src/vcf_histogram.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 90%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -MF CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d -o CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_bcf_generator.cc [ 90%] Linking CXX executable test_expressions cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_expressions.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test_expressions.dir/link.d CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o -o test_expressions ../core/libgenomicsdb-tiledb.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libuuid.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libcurl.so -ldl /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 90%] Built target test_expressions make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 91%] Building CXX object example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -MF CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d -o CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_importer.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_bcf_generator.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_bcf_generator.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Linking CXX executable gt_mpi_gather cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gt_mpi_gather.dir/link.txt --verbose=1 In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_importer.cc:26: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/example/src/test_genomicsdb_importer.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -MF CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o.d -o CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_non_diploid_mapper.cc [ 92%] Linking CXX executable test_genomicsdb_bcf_generator cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_bcf_generator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/gt_mpi_gather.dir/link.d CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -o gt_mpi_gather -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 92%] Built target gt_mpi_gather make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -Wl,--dependency-file=CMakeFiles/test_genomicsdb_bcf_generator.dir/link.d CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -o test_genomicsdb_bcf_generator -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 92%] Built target test_genomicsdb_bcf_generator [ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:29: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api/tiledb.h:44, from /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api/tiledb_utils.h:39, from /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:25: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_non_diploid_mapper.cc:26: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/catch2/interfaces/catch_interfaces_capture.hpp:11, from /usr/include/catch2/benchmark/catch_benchmark.hpp:19, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_non_diploid_mapper.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Linking CXX executable create_genomicsdb_workspace cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_genomicsdb_workspace.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/create_genomicsdb_workspace.dir/link.d CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o -o create_genomicsdb_workspace -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 92%] Built target create_genomicsdb_workspace [ 92%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -MF CMakeFiles/ctests.dir/src/test_multid_vector.cc.o.d -o CMakeFiles/ctests.dir/src/test_multid_vector.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_multid_vector.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:24: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:23: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Linking CXX executable vcfdiff cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdiff.dir/link.txt --verbose=1 [ 93%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBQuery.cc [ 93%] Linking CXX executable test_genomicsdb_demo cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_demo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/vcfdiff.dir/link.d CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -o vcfdiff -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 93%] Built target vcfdiff [ 94%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o -MF CMakeFiles/ctests.dir/src/test_pb.cc.o.d -o CMakeFiles/ctests.dir/src/test_pb.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_pb.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_multid_vector.cc:27: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/catch2/interfaces/catch_interfaces_capture.hpp:11, from /usr/include/catch2/benchmark/catch_benchmark.hpp:19, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_multid_vector.cc:24: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Linking CXX executable consolidate_genomicsdb_array cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/consolidate_genomicsdb_array.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -Wl,--dependency-file=CMakeFiles/test_genomicsdb_demo.dir/link.d CMakeFiles/test_genomicsdb_demo.dir/src/test_genomicsdb_demo.cc.o -o test_genomicsdb_demo -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 95%] Built target test_genomicsdb_demo [ 96%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o -MF CMakeFiles/ctests.dir/src/test_logger.cc.o.d -o CMakeFiles/ctests.dir/src/test_logger.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_logger.cc cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc [ 96%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIC -MD -MT src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -MF CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d -o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_jni_init.cc [ 96%] Linking CXX executable vcf_histogram cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf_histogram.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/consolidate_genomicsdb_array.dir/link.d CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -o consolidate_genomicsdb_array -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o -MF CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o.d -o CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc [ 96%] Built target consolidate_genomicsdb_array [ 97%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -MF CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d -o CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_htslib_plugin.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc:25: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jlong Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniInitializeGenomicsDBImporterObject(JNIEnv*, jobject, jstring, jint)': /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:102:3: warning: control reaches end of non-void function [-Wreturn-type] 102 | } | ^ /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jlong Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniSetupGenomicsDBLoader(JNIEnv*, jobject, jlong, jstring)': /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:159:3: warning: control reaches end of non-void function [-Wreturn-type] 159 | } | ^ /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jboolean Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniImportBatch(JNIEnv*, jobject, jlong, jlongArray)': /build/reproducible-path/genomicsdb-1.5.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:231:3: warning: control reaches end of non-void function [-Wreturn-type] 231 | } | ^ [ 98%] Linking CXX executable vcf2genomicsdb cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/vcf_histogram.dir/link.d CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -o vcf_histogram -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 98%] Built target vcf_histogram [ 98%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o -MF CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o.d -o CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_alleles_combiner.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:31: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/catch2/interfaces/catch_interfaces_capture.hpp:11, from /usr/include/catch2/benchmark/catch_benchmark.hpp:19, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:29: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o -MF CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d -o CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_gt_remapper.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/vcf2genomicsdb.dir/link.d CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -o vcf2genomicsdb -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 98%] Built target vcf2genomicsdb [ 99%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o -MF CMakeFiles/ctests.dir/src/test_bgen.cc.o.d -o CMakeFiles/ctests.dir/src/test_bgen.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_bgen.cc [ 99%] Linking CXX executable api_tests cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/api_tests.dir/link.txt --verbose=1 [ 99%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_query_variants.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_query_variants.cc.o -MF CMakeFiles/ctests.dir/src/test_query_variants.cc.o.d -o CMakeFiles/ctests.dir/src/test_query_variants.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_query_variants.cc [ 99%] Linking CXX executable test_genomicsdb_importer cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_importer.dir/link.txt --verbose=1 [ 99%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.4/tests/\" -DGENOMICSDB_VERSION=\"1.5.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core/include/c_api -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/ctests.dir/src/test_mem_utils.cc.o -MF CMakeFiles/ctests.dir/src/test_mem_utils.cc.o.d -o CMakeFiles/ctests.dir/src/test_mem_utils.cc.o -c /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_mem_utils.cc In file included from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_query_variants.cc:31: /build/reproducible-path/genomicsdb-1.5.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/catch2/interfaces/catch_interfaces_capture.hpp:11, from /usr/include/catch2/benchmark/catch_benchmark.hpp:19, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/src/test_query_variants.cc:28: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -Wl,--dependency-file=CMakeFiles/api_tests.dir/link.d CMakeFiles/api_tests.dir/src/ctest_main.cc.o CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o -o api_tests -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/cmake -E tar xzf /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp/../inputs/test.tgz make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 99%] Built target api_tests /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -Wl,--dependency-file=CMakeFiles/test_genomicsdb_importer.dir/link.d CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -o test_genomicsdb_importer -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 99%] Built target test_genomicsdb_importer [ 99%] Linking CXX shared library libgenomicsdbjni.so cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdbjni.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,--dependency-file=CMakeFiles/genomicsdbjni.dir/link.d -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -shared -Wl,-soname,libgenomicsdbjni.so -o libgenomicsdbjni.so CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib libgenomicsdb.so.1.5.4 ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 99%] Built target genomicsdbjni [ 99%] Linking CXX executable vcf2genomicsdb_init cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2genomicsdb_init.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -pie -Wl,--dependency-file=CMakeFiles/vcf2genomicsdb_init.dir/link.d CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -o vcf2genomicsdb_init -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 99%] Built target vcf2genomicsdb_init [100%] Linking CXX executable ctests cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ctests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -Wl,-z,relro -Wl,-z,now -z noexecstack -z relro -z now -Wl,--dependency-file=CMakeFiles/ctests.dir/link.d CMakeFiles/ctests.dir/src/ctest_main.cc.o CMakeFiles/ctests.dir/src/test_config.cc.o CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o CMakeFiles/ctests.dir/src/test_multid_vector.cc.o CMakeFiles/ctests.dir/src/test_pb.cc.o CMakeFiles/ctests.dir/src/test_logger.cc.o CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o CMakeFiles/ctests.dir/src/test_bgen.cc.o CMakeFiles/ctests.dir/src/test_query_variants.cc.o CMakeFiles/ctests.dir/src/test_mem_utils.cc.o -o ctests -Wl,-rpath,/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib:/usr/lib/aarch64-linux-gnu/openmpi/lib ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/aarch64-linux-gnu/librt.a /usr/lib/aarch64-linux-gnu/libprotobuf.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl /usr/lib/aarch64-linux-gnu/libfmt.so.10.1.0 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libmuparserx.so /usr/lib/aarch64-linux-gnu/libbz2.so /usr/lib/aarch64-linux-gnu/liblzma.so /usr/lib/aarch64-linux-gnu/libcurl.so /usr/lib/aarch64-linux-gnu/libssl.so /usr/lib/aarch64-linux-gnu/libcrypto.so /usr/lib/aarch64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [100%] Built target ctests make[3]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' # Building the Java part with Maven. dh_auto_build --buildsystem=maven /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/genomicsdb-1.5.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.4/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.4/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ---------------------< org.genomicsdb:genomicsdb >---------------------- [INFO] Building org.genomicsdb:genomicsdb 1.5.4 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact com.googlecode.json-simple:json-simple:jar:debian has been relocated to com.github.cliftonlabs:json-simple:jar:debian [INFO] [INFO] --- antrun:3.1.0:run (exec-protoc) @ genomicsdb --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java [INFO] Executed tasks [INFO] [INFO] --- build-helper:3.3.0:add-source (add-source) @ genomicsdb --- [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/src/main/scala added. [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.4/src/main/resources [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ genomicsdb --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 30 source files with javac [debug target 17] to build/classes [WARNING] system modules path not set in conjunction with -source 17 [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java:[37,14] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[79,39] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[206,31] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[483,84] PARSER in org.genomicsdb.model.Coordinates.GenomicsDBColumnOrInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[5485,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[4407,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[10171,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7553,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7594,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7635,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[792,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[3035,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[3987,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBVidMapProto.java:[93,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBCallsetsMapProto.java:[139,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[177,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[2228,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[2269,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/exception/GenomicsDBException.java:[28,8] serializable class org.genomicsdb.exception.GenomicsDBException has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[50,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.Pair has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[70,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.VariantCall has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[76,25] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[110,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.Interval has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[112,23] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/ImportConfig.java:[76,36] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,50] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[160,28] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[333,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[333,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[334,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[334,30] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[336,9] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[336,41] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[338,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[338,36] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[342,17] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[342,40] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[462,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[462,45] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[483,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[483,41] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[690,94] found raw type: java.util.concurrent.CompletableFuture missing type arguments for generic class java.util.concurrent.CompletableFuture [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[224,46] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[99,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[109,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[54,27] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[139,58] previous possible 'this' escape happens here via invocation [INFO] [INFO] --- antrun:3.1.0:run (copy-native-libs) @ genomicsdb --- [INFO] Executing tasks [WARNING] [exec] The command attribute is deprecated. [exec] Please use the executable attribute and nested arg elements. [INFO] [exec] cp: cannot stat '/build/reproducible-path/genomicsdb-1.5.4/build/src/main/libtiledbgenomicsdb.dylib': No such file or directory [INFO] [exec] Result: 1 [WARNING] [exec] The command attribute is deprecated. [exec] Please use the executable attribute and nested arg elements. [INFO] [exec] cp: cannot stat '/build/reproducible-path/genomicsdb-1.5.4/build/src/main/libtiledbgenomicsdb.so': No such file or directory [INFO] [exec] Result: 1 [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.4/src/test/resources [INFO] [INFO] --- antrun:3.1.0:run (unzip-test-artifacts) @ genomicsdb --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/reproducible-path/genomicsdb-1.5.4/build/test [INFO] [copy] Copying 1 file to /build/reproducible-path/genomicsdb-1.5.4/build/test [INFO] [gunzip] Expanding test.tar.gz to /build/reproducible-path/genomicsdb-1.5.4/build/test/test.tar [INFO] [untar] Expanding: /build/reproducible-path/genomicsdb-1.5.4/build/test/test.tar into /build/reproducible-path/genomicsdb-1.5.4/build/test [INFO] Executed tasks [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ genomicsdb --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 12 source files with javac [debug target 17] to build/test-classes [WARNING] system modules path not set in conjunction with -source 17 [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] No processor claimed any of these annotations: /org.testng.annotations.BeforeClass,/org.testng.annotations.Test,/org.testng.annotations.DataProvider,/org.testng.annotations.BeforeMethod,/org.testng.annotations.AfterMethod [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,38] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,13] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,39] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,44] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[201,18] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[257,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[289,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[322,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[362,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[398,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[443,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[482,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[536,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ genomicsdb --- [INFO] Tests are skipped. [INFO] [INFO] --- jar:3.3.0:jar (default-jar) @ genomicsdb --- [INFO] Building jar: /build/reproducible-path/genomicsdb-1.5.4/build/genomicsdb-1.5.4.jar [INFO] [INFO] --- jar:3.3.0:jar (main) @ genomicsdb --- [INFO] Building jar: /build/reproducible-path/genomicsdb-1.5.4/build/genomicsdb-1.5.4-main.jar [INFO] [INFO] --- jar:3.3.0:jar (spark) @ genomicsdb --- [INFO] Building jar: /build/reproducible-path/genomicsdb-1.5.4/build/genomicsdb-1.5.4-spark.jar [INFO] [INFO] --- antrun:3.1.0:run (replace-core-jar) @ genomicsdb --- [INFO] Executing tasks [INFO] [move] Moving 1 file to /build/reproducible-path/genomicsdb-1.5.4/build [INFO] [move] Moving 1 file to /build/reproducible-path/genomicsdb-1.5.4/build [INFO] Executed tasks [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7.195 s [INFO] Finished at: 2025-04-25T01:46:36-12:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' dh_auto_test -a || true cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: test_array_schema 1: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_schema 1: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 1: Test timeout computed to be: 10000000 test 2 Start 2: test_print_array_schema 2: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_print_array_schema 2: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 2: Test timeout computed to be: 10000000 test 3 Start 3: test_print_book_keeping 3: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_print_book_keeping 3: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 3: Test timeout computed to be: 10000000 test 4 Start 4: test_sparse_array_benchmark 4: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_benchmark 4: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 4: Test timeout computed to be: 10000000 test 5 Start 5: test_array_iterator 5: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_iterator 5: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 5: Test timeout computed to be: 10000000 test 6 Start 6: test_array_schema_api 6: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_schema_api 6: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 6: Test timeout computed to be: 10000000 test 7 Start 7: test_dense_array_api 7: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_dense_array_api 7: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 7: Test timeout computed to be: 10000000 test 8 Start 8: test_sparse_array_api 8: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_api 8: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 8: Test timeout computed to be: 10000000 test 9 Start 9: test_tiledb_utils 9: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_tiledb_utils 9: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 9: Test timeout computed to be: 10000000 test 10 Start 10: test_codec 10: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_codec 10: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 10: Test timeout computed to be: 10000000 test 11 Start 11: test_codec_filter 11: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_codec_filter 11: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 11: Test timeout computed to be: 10000000 test 12 Start 12: test_expressions 12: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_expressions 12: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 12: Test timeout computed to be: 10000000 1: Randomness seeded to: 2628683690 1: [TileDB::ArraySchema] Error: Cannot set attributes; No attributes given. 1: [TileDB::ArraySchema] Error: Cannot set attributes; The number of attributes must be positive. 1: [TileDB::ArraySchema] Error: Cannot set attributes; Duplicate attribute names. 1: [TileDB::ArraySchema] Error: Cannot set cell order; Invalid cell order. 1: [TileDB::ArraySchema] Error: Unsupported. For a given VAR attribute, both compression and offsets_compression have to either have compression or not 1: . 1: [TileDB::ArraySchema] Error: Cannot set dimensions; No dimensions given. 1: [TileDB::ArraySchema] Error: Cannot set dimensions; The number of dimensions must be positive. 1: [TileDB::ArraySchema] Error: Cannot set dimensions; Duplicate dimension names. 1: [TileDB::ArraySchema] Error: Cannot set dimensions; Attribute name same as dimension name. 1: [TileDB::ArraySchema] Error: Cannot set types; Types not provided. 1: [TileDB::ArraySchema] Error: Cannot set types; Invalid type. 1: [TileDB::ArraySchema] Error: Cannot set domain; Domain not provided. 1: [TileDB::ArraySchema] Error: Cannot set tile order; Invalid tile order. 1: Array Schema Version: 1: 2 1: Array workspace: 1: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 1: Array name: 1: 1: Dimension names: 1: dim1 1: dim2 1: Attribute names: 1: test_attr 1: test_attr1 1: Domain: 1: dim1: [0,99] 1: dim2: [0,99] 1: Types: 1: test_attr: int32[1] 1: test_attr1: int32[var] 1: Coordinates: int32 1: Cell sizes (in bytes): 1: test_attr: 4 1: test_attr1: var 1: Coordinates: 8 1: Dense: 1: false 1: Tile types: 1: irregular 1: Tile order: 1: - 1: Cell order: 1: column-major 1: Capacity: 1: 10000 1: Tile extents: 1: - 1: Compression for test_attr 1: Type = GZIP 1: Level= -1 1: Compression for test_attr1 1: Type = GZIP 1: Level= -1 1: Compression for offsets of test_attr1 1: Type = GZIP + DELTA_ENCODE 1: Level= -1 1: Compression for Coordinates: 1: Type = GZIP 1: Array Schema Version: 1: 2 1: Array name: 1: this_array 1: Dimension names: 1: one_dim 1: Attribute names: 1: this_attribute 1: Domain: 1: one_dim: [1,100] 1: Types: 1: this_attribute: int32[1] 1: Coordinates: int32 1: Cell sizes (in bytes): 1: this_attribute: 4 1: Coordinates: 4 1: Dense: 1: false 1: Tile types: 1: regular 1: Tile order: 1: row-major 1: Cell order: 1: row-major 1: Capacity: 1: - 1: Tile extents: 1: one_dim: 25 1: Compression for this_attribute 1: Type = NONE 1: Level= -1 1: Compression for Coordinates: 1: Type = NONE 1: Array Schema Version: 1: 2 1: Array name: 1: this_array 1: Dimension names: 1: one_dim 1: Attribute names: 1: this_attribute 1: Domain: 1: one_dim: [1,100] 1: Types: 1: this_attribute: int32[1] 1: Coordinates: int32 1: Cell sizes (in bytes): 1: this_attribute: 4 1: Coordinates: 4 1: Dense: 1: false 1: Tile types: 1: regular 1: Tile order: 1: row-major 1: Cell order: 1: row-major 1: Capacity: 1: - 1: Tile extents: 1: one_dim: 25 1: Compression for this_attribute 1: Type = NONE 1: Level= -1 1: Compression for Coordinates: 1: Type = NONE 1: Array Schema Version: 1: 2 1: Array name: 1: this_array_64 1: Dimension names: 1: one_dim_64 1: Attribute names: 1: this_attribute 1: Domain: 1: one_dim_64: [1,1] 1: Types: 1: this_attribute: int64[1] 1: Coordinates: int64 1: Cell sizes (in bytes): 1: this_attribute: 8 1: Coordinates: 8 1: Dense: 1: false 1: Tile types: 1: regular 1: Tile order: 1: row-major 1: Cell order: 1: row-major 1: Capacity: 1: - 1: Tile extents: 1: one_dim_64: 25 1: Compression for this_attribute 1: Type = NONE 1: Level= -1 1: Compression for Coordinates: 1: Type = NONE 1: =============================================================================== 1: All tests passed (43 assertions in 7 test cases) 1: 2: No arguments specified 2: Usage: test_print_array_schema /path/to/TileDBArray 3: No arguments specified 3: Usage: test_print_book_keeping /path/to/TileDBArray/ 4: Randomness seeded to: 4268692392 4: =============================================================================== 4: test cases: 1 | 1 passed 4: assertions: - none - 4: 5: Randomness seeded to: 2024399227 5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR 5: 5: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5: test_array_iterator is a Catch2 v3.7.1 host application. 5: Run with -? for options 5: 5: ------------------------------------------------------------------------------- 5: Test sparse array iterator 5: ------------------------------------------------------------------------------- 5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194 5: ............................................................................... 5: 5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194: FAILED: 5: {Unknown expression after the reported line} 5: due to a fatal error condition: 5: SIGSEGV - Segmentation violation signal 5: 5: =============================================================================== 5: test cases: 1 | 1 failed 5: assertions: 7 | 6 passed | 1 failed 5: 6: Randomness seeded to: 2894233546 6: 6: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6: test_array_schema_api is a Catch2 v3.7.1 host application. 6: Run with -? for options 6: 6: ------------------------------------------------------------------------------- 6: Test array schema backward compatibility 2 6: ------------------------------------------------------------------------------- 6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:349 6: ............................................................................... 6: 6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:368: FAILED: 6: CHECK( array_schema.compression_level_[1] == -1 ) 6: with expansion: 6: 255 == -1 6: 6: =============================================================================== 6: test cases: 13 | 12 passed | 1 failed 6: assertions: 335 | 334 passed | 1 failed 6: 1/22 Test #1: test_array_schema ................ Passed 0.06 sec 2/22 Test #2: test_print_array_schema .......... Passed 0.06 sec 3/22 Test #3: test_print_book_keeping .......... Passed 0.05 sec 4/22 Test #4: test_sparse_array_benchmark ...... Passed 0.05 sec 5/22 Test #5: test_array_iterator ..............***Exception: SegFault 0.05 sec Randomness seeded to: 2024399227 [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test_array_iterator is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- Test sparse array iterator ------------------------------------------------------------------------------- ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194 ............................................................................... ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:194: FAILED: {Unknown expression after the reported line} due to a fatal error condition: SIGSEGV - Segmentation violation signal =============================================================================== test cases: 1 | 1 failed assertions: 7 | 6 passed | 1 failed 6/22 Test #6: test_array_schema_api ............***Failed 0.05 sec Randomness seeded to: 2894233546 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ test_array_schema_api is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- Test array schema backward compatibility 2 ------------------------------------------------------------------------------- ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:349 ............................................................................... ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:368: FAILED: CHECK( array_schema.compression_level_[1] == -1 ) with expansion: 255 == -1 =============================================================================== test cases: 13 | 12 passed | 1 failed assertions: 335 | 334 passed | 1 failed 9: Randomness seeded to: 3447815344 9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestOuY8zR/WORKSPACE.nonexistent does not exist 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestoYEcGe/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTestoYEcGe/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestD1exiU/WORKSPACE errno=2(No such file or directory) 9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestweZjCi/test_file 9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestweZjCi/test_file 11: Randomness seeded to: 2407262389 11: [TileDB::CodecFilter] Error: virtual method should be overridden. 11: [TileDB::CodecFilter] Error: virtual method should be overridden. 11: [TileDB::CodecFilter] Error: virtual method should be overridden. 11: [TileDB::CodecFilter] Error: virtual method should be overridden. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Delta Encoding should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: [TileDB::CodecFilter] Error: Tile size to pre-compression filter Bit Shuffle should be a multiple of sizeof type. 11: =============================================================================== 11: All tests passed (192 assertions in 2 test cases) 11: 7/22 Test #11: test_codec_filter ................ Passed 0.03 sec 10: Randomness seeded to: 382348771 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR 10: [TileDB::Codec] Error: Could not decompress with GZIP. 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_BUF_ERROR 10: [TileDB::Codec] Error: Could not decompress with GZIP. 10: [TileDB::utils] Error: (gzip_handle_error) Cannot decompress with GZIP: inflate error: Z_DATA_ERROR 10: [TileDB::Codec] Error: Could not decompress with GZIP. 10: [TileDB::Codec] Error: Codec for compression type=15 has already been registered. 10: =============================================================================== 10: All tests passed (31 assertions in 5 test cases) 10: 8/22 Test #10: test_codec ....................... Passed 0.04 sec 12: Randomness seeded to: 2010800107 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Index to variable "a1" is out of bounds. 12: [TileDB::Expression] Error: (init) Attribute a2 in expression filter not present in the array schema 12: [TileDB::Expression] Error: (init) Parser SetExpr error for expression 'a1 === 22': Unexpected operator "=" found at position 5. 12: [TileDB::Expression] Error: (evaluate) Initialization not completed 12: [TileDB::Expression] Error: (evaluate_cell) Initialization not completed 12: [TileDB::Expression] Error: (evaluate_cell) Only expressions evaluating to booleans is supported test 13 Start 13: test_filter_api 13: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_filter_api 13: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 13: Test timeout computed to be: 10000000 test 14 Start 14: test_mem_utils 14: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_mem_utils 14: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 14: Test timeout computed to be: 10000000 test 15 Start 15: test_uri 15: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_uri 15: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 15: Test timeout computed to be: 10000000 test 16 Start 16: test_utils 16: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_utils 16: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 16: Test timeout computed to be: 10000000 test 17 Start 17: test_posixfs 17: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_posixfs 17: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 17: Test timeout computed to be: 10000000 test 18 Start 18: test_storage_buffer 18: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_storage_buffer 18: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test 18: Test timeout computed to be: 10000000 12: [TileDB::Expression] Error: (init) Parser SetExpr error for expression 'resolve(a1) &= ""': Too few parameters passed to function "resolve". 12: [TileDB::Expression] Error: (init) Expression parsing for dense arrays not yet implemented 12: =============================================================================== 12: All tests passed (3334 assertions in 83 test cases) 12: test 19 Start 19: ci_tests 19: Test command: /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples/run_examples.sh "&&" "echo" "Running diff with expected_results" "&&" "diff" "log" "/build/reproducible-path/genomicsdb-1.5.4/examples/expected_results" 19: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples 19: Test timeout computed to be: 10000000 test 20 Start 20: ctests 20: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests "-d" "yes" 20: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp 20: Test timeout computed to be: 10000000 14: Randomness seeded to: 3430672555 14: Fri Apr 25 01:46:38 2025 Memory stats Tracking memory usage START size=6MB resident=1MB share=1MB text=604KB lib=0 data=540KB dt=0 15: Randomness seeded to: 3509577965 15: =============================================================================== 15: All tests passed (113 assertions in 1 test case) 15: 16: Randomness seeded to: 1413500584 16: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; invalid input buffer format 16: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; output buffer overflow 16: [TileDB::utils] Error: (RLE_compress_coords_row) Failed compressing coordinates with RLE; invalid buffer format 16: [TileDB::utils] Error: (RLE_compress_coords_row) Filed compressing coordinates with RLE; output buffer overflow 16: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; invalid buffer format 16: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; output buffer overflow 16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/non-existent-dir/file errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-dir/file errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=/non-existent-dir/file errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/non-existent-dir/file errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=/non-existent-dir/dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=/non-existent-dir/old errno=2(No such file or directory) 16: =============================================================================== 16: All tests passed (86 assertions in 6 test cases) 16: 9/22 Test #12: test_expressions ................. Passed 0.07 sec 10/22 Test #15: test_uri ......................... Passed 0.03 sec 11/22 Test #16: test_utils ....................... Passed 0.03 sec test 21 Start 21: api_tests 21: Test command: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/api_tests "-d" "yes" 21: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp 21: Test timeout computed to be: 10000000 test 22 Start 22: tools_tests 22: Test command: /build/reproducible-path/genomicsdb-1.5.4/tests/test_tools.sh "/build/reproducible-path/genomicsdb-1.5.4/tests/inputs/vcfs" "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools" "1" 22: Working Directory: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools 22: Test timeout computed to be: 10000000 17: Randomness seeded to: 3286673439 17: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTestNOGr2J/test_posixfs_dirdir 17: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/foo errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestNOGr2J/test_posixfs_dirdir errno=21(Is a directory) 17: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestNOGr2J/test_posixfs_dirdir errno=21(Is a directory) 17: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-dir errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=non-existent-dir errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=non-existent-dir errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=non-existent-dir errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestNSxjZ8/test_posixfs_dirfile/foo1 errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestCLxd3J/test_posixfs_dirread_write/foo 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestCLxd3J/test_posixfs_dirread_write/foo 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestCLxd3J/test_posixfs_dirread_write/foo 17: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-dir/foo errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=non-existent-dir/foo errno=2(No such file or directory) 17: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo 17: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_sync 17: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_no_close 17: =============================================================================== 17: All tests passed (258 assertions in 11 test cases) 17: 13: Randomness seeded to: 103601481 13: =============================================================================== 13: All tests passed (288 assertions in 3 test cases) 13: 12/22 Test #13: test_filter_api .................. Passed 0.06 sec 18: Randomness seeded to: 1813837003 18: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestn1XEab/test-file 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTestn1XEab/test-file-non-existent errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestn1XEab/test-file 18: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestn1XEab/test-file 18: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied) 18: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (gzip_write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (write_buffer) Cannot compress and/or write bytes path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied) 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/non-existent-file errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (write_buffer) Compression type=1000 not supported in StorageBuffer 18: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=2(No such file or directory) 18: [TileDB::StorageBuffer] Error: (read_buffer) Compression type=1000 for read_buffer not supported for CompressedStorageBuffer 18: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestzOsP4I/compressed_foo 13/22 Test #17: test_posixfs ..................... Passed 0.05 sec 19: Example 1: Running ./tiledb_workspace_group_create... 21: Randomness seeded to: 1906762867 21: 0.001 s: utils 21: 0.000 s: api empty_args 19: Example 1: Done running ./tiledb_workspace_group_create 19: Example 2: Running ./tiledb_ls_workspaces... 19: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=&& errno=2(No such file or directory) 19: Example 2: Done running ./tiledb_ls_workspaces 21: 0.021 s: api query_variants direct DP 19: Example 3: Running ./tiledb_array_create_dense... 21: 0.007 s: api query_variants direct DP with huge row range 20: 01:46:38.550 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.551 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.551 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: Randomness seeded to: 398393808 20: 0.004 s: Check loader configuration with json file 20: 01:46:38.552 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.552 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.552 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 0.001 s: Check configuration with json file 20: 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.553 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 0.001 s: Check configuration with json file and shared posifs optim 20: 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.553 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 0.001 s: Compare configuration with json file and string 20: 0.000 s: genotype_ordering haploid_5_alleles 20: 0.000 s: genotype_ordering diploid_2_alleles 20: 0.000 s: genotype_ordering diploid_3_alleles 20: 0.000 s: genotype_ordering diploid_4_alleles 20: 0.000 s: genotype_ordering triploid_2_alleles 20: 0.000 s: genotype_ordering triploid_3_alleles 20: 0.000 s: genotype_ordering triploid_4_alleles 20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles 20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF 20: 0.000 s: multid_vector 2D_test 20: 0.000 s: multid_vector 3D_test 20: 0.000 s: multid_vector 2D_test_with_missing_values 20: 0.000 s: multid_vector 2D_float_test 20: 0.000 s: multid_vector 2D_tuple_test 20: 0.000 s: pb_query_config_test 21: 0.006 s: api query_variants direct DP with huge disjoint row ranges 19: Example 3: Done running ./tiledb_array_create_dense 20: 0.001 s: pb_vid_mapping_test 20: 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 Contig/chromosome 2 begins at TileDB column 249250601 and intersects with contig/chromosome 1 that spans columns [0, 249250620] 20: 0.001 s: pb_overlapping_vid_mapping_test 20: 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 This is a test 20: 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 This is a test 20: 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 This is a test 20: 01:46:38.556 DEBUG NativeGenomicsDB - pid=854531 tid=854531 This is a test 20: This is a test 20: This is a test 20: This is a test 20: This is a test 20: This is a once_only test 20: Trying format Hello1 Hello2 20: 0.000 s: test logger 20: 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 i=1 str=This is a test 20: 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 i=2 str=This is a test 20: 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 i=3 str=This is a test 20: 01:46:38.556 DEBUG NativeGenomicsDB - pid=854531 tid=854531 i=4 str=This is a test 20: 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 i=6 str=This is a once_only test 20: 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 i=7 str=This is a once_only test 20: 0.000 s: test logger format 20: 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 i=1 str=This is a test 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Native Stack Trace: 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5a0) [0xaaaae2dfa5a0] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 20: 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Native Stack Trace: 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5cc) [0xaaaae2dfa5cc] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 20: 0.001 s: test logger exceptions 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cea4) [0xaaaae2dfcea4] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ce80) [0xaaaae2dfce80] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] 20: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] 20: /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 20: This is a test 20: 0.000 s: test explicit logger 20: 01:46:38.557 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.557 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.558 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 19: Example 4: Running ./tiledb_array_create_sparse... 21: 0.011 s: api query_variants direct DP with range composed of multiple points 20: 0.008 s: gvcf iterator 20: 01:46:38.566 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.566 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.566 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 19: Example 4: Done running ./tiledb_array_create_sparse 19: Example 5: Running ./tiledb_array_primitive... 21: 0.009 s: api query_variants direct DP with range composed of overlapping ranges 20: 0.009 s: columnar_gvcf_iterator_test 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f 20: [TileDB] Error: No TileDB support for URL=dfdfd://ddd. 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 htslib_plugin could not open dfdfd://ddd 20: No TileDB support for URL=dfdfd://ddd 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f/foo 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f/foo 20: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin write /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) 20: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) 20: 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) 20: 0.000 s: test htslib plugin 20: 0.000 s: alleles_combiner 20: 0.000 s: gt_remapper 21: 01:46:38.575 ERROR NativeGenomicsDB - pid=854532 tid=854532 Query interval 0:-100-1 is out of bounds 21: 0.003 s: api query_variants direct DP with invalid row range 19: Array name: my_workspace/dense_arrays/my_array_A 19: Attributes: a1 a2 a3 19: The array is dense 19: Array name: my_workspace/sparse_arrays/my_array_B 19: Attributes: a1 a2 a3 19: The array is sparse 19: Example 5: Done running ./tiledb_array_primitive 19: Example 6: Running ./tiledb_array_write_dense_1... 21: 0.013 s: api query_variants direct DP and GT 19: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR 19: [TileDB::Codec] Error: Could not compress with GZIP. 19: [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__d7767ddc-ca3c-4883-9d2c-c75d399d3224281472895557664_1745588798591/a1.tdb. 19: [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__d7767ddc-ca3c-4883-9d2c-c75d399d3224281472895557664_1745588798591/a1.tdb[Examples::./genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc] Runtime Error. 19: 19: Exit Status=255. Quitting execution of run_examples.sh 14/22 Test #19: ci_tests .........................***Failed 0.13 sec Example 1: Running ./tiledb_workspace_group_create... Example 1: Done running ./tiledb_workspace_group_create Example 2: Running ./tiledb_ls_workspaces... [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=&& errno=2(No such file or directory) Example 2: Done running ./tiledb_ls_workspaces Example 3: Running ./tiledb_array_create_dense... Example 3: Done running ./tiledb_array_create_dense Example 4: Running ./tiledb_array_create_sparse... Example 4: Done running ./tiledb_array_create_sparse Example 5: Running ./tiledb_array_primitive... Array name: my_workspace/dense_arrays/my_array_A Attributes: a1 a2 a3 The array is dense Array name: my_workspace/sparse_arrays/my_array_B Attributes: a1 a2 a3 The array is sparse Example 5: Done running ./tiledb_array_primitive Example 6: Running ./tiledb_array_write_dense_1... [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR [TileDB::Codec] Error: Could not compress with GZIP. [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__d7767ddc-ca3c-4883-9d2c-c75d399d3224281472895557664_1745588798591/a1.tdb. [TileDB::WriteState] Error: Cannot compress tile for /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__d7767ddc-ca3c-4883-9d2c-c75d399d3224281472895557664_1745588798591/a1.tdb[Examples::./genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc] Runtime Error. Exit Status=255. Quitting execution of run_examples.sh 21: 0.012 s: api query_variants direct DP and GT with PP 21: 01:46:38.602 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.602 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.602 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.608 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.608 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.608 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.613 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.613 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.613 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.012 s: api query_variants with json 21: 01:46:38.614 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.614 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.614 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock 21: 01:46:38.619 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.619 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.620 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.625 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.012 s: api query variants with json string 21: 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.626 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.626 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.005 s: api query variants with enabled shared posixfs optimizations 21: ---------------- 21: Interval:[0,9223372036854775806] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] DP:76 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] DP:76 20: 20: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 20: ctests is a Catch2 v3.7.1 host application. 20: Run with -? for options 20: 20: ------------------------------------------------------------------------------- 20: test bgen 20: ------------------------------------------------------------------------------- 20: ./src/test/cpp/src/test_bgen.cc:11 20: ............................................................................... 20: 20: ./src/test/cpp/src/test_bgen.cc:11: FAILED: 20: due to unexpected exception with message: 20: Direct - first BGEN test output did not match reference output 20: 20: 0.000 s: test bgen 20: 01:46:38.640 ERROR NativeGenomicsDB - pid=854531 tid=854531 VariantStorageManagerException exception : Could not open workspace 20: 01:46:38.641 ERROR NativeGenomicsDB - pid=854531 tid=854531 Could not open array non_existent_array in workspace /tmp/GenomicsDBrgMhiQ/ws 20: 01:46:38.641 ERROR NativeGenomicsDB - pid=854531 tid=854531 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDBrgMhiQ/ws 20: 0.000 s: constructor 20: 01:46:38.641 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 20: 01:46:38.641 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 01:46:38.642 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 01:46:38.645 ERROR NativeGenomicsDB - pid=854531 tid=854531 Invalid query attribute : non_existent_attribute 21: 0.015 s: api query_variant_calls direct 20: 0.005 s: test basic queries 20: 01:46:38.646 INFO NativeGenomicsDB - pid=854531 tid=854531 Mem usage Check basic memory usage rss=46M 20: 0.000 s: check basic memory usage 20: =============================================================================== 20: test cases: 34 | 33 passed | 1 failed 20: assertions: 1440 | 1439 passed | 1 failed 20: 20: 01:46:38.646 DEBUG NativeGenomicsDB - pid=854531 tid=854531 Deleting htslib_fs_adapter tiledb_ctx_map 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 15/22 Test #20: ctests ...........................***Failed 0.18 sec 01:46:38.550 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.551 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.551 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name Randomness seeded to: 398393808 0.004 s: Check loader configuration with json file 01:46:38.552 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.552 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.552 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.001 s: Check configuration with json file 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.553 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.001 s: Check configuration with json file and shared posifs optim 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.553 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.553 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.001 s: Compare configuration with json file and string 0.000 s: genotype_ordering haploid_5_alleles 0.000 s: genotype_ordering diploid_2_alleles 0.000 s: genotype_ordering diploid_3_alleles 0.000 s: genotype_ordering diploid_4_alleles 0.000 s: genotype_ordering triploid_2_alleles 0.000 s: genotype_ordering triploid_3_alleles 0.000 s: genotype_ordering triploid_4_alleles 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF 0.000 s: multid_vector 2D_test 0.000 s: multid_vector 3D_test 0.000 s: multid_vector 2D_test_with_missing_values 0.000 s: multid_vector 2D_float_test 0.000 s: multid_vector 2D_tuple_test 0.000 s: pb_query_config_test 0.001 s: pb_vid_mapping_test 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 Contig/chromosome 2 begins at TileDB column 249250601 and intersects with contig/chromosome 1 that spans columns [0, 249250620] 0.001 s: pb_overlapping_vid_mapping_test 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 This is a test 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 This is a test 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 This is a test 01:46:38.556 DEBUG NativeGenomicsDB - pid=854531 tid=854531 This is a test This is a test This is a test This is a test This is a test This is a once_only test Trying format Hello1 Hello2 0.000 s: test logger 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 i=1 str=This is a test 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 i=2 str=This is a test 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 i=3 str=This is a test 01:46:38.556 DEBUG NativeGenomicsDB - pid=854531 tid=854531 i=4 str=This is a test 01:46:38.556 INFO NativeGenomicsDB - pid=854531 tid=854531 i=6 str=This is a once_only test 01:46:38.556 WARN NativeGenomicsDB - pid=854531 tid=854531 i=7 str=This is a once_only test 0.000 s: test logger format 01:46:38.556 ERROR NativeGenomicsDB - pid=854531 tid=854531 i=1 str=This is a test 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Native Stack Trace: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5a0) [0xaaaae2dfa5a0] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Test Exception 01:46:38.557 ERROR NativeGenomicsDB - pid=854531 tid=854531 Native Stack Trace: /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6a5cc) [0xaaaae2dfa5cc] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] 0.001 s: test logger exceptions /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cea4) [0xaaaae2dfcea4] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x7b768) [0xaaaae2e0b768] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ce80) [0xaaaae2dfce80] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2277cc) [0xaaaae2fb77cc] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x228180) [0xaaaae2fb8180] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x2285b4) [0xaaaae2fb85b4] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe1d8) [0xaaaae2f8e1d8] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x1fe724) [0xaaaae2f8e724] /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x40250) [0xaaaae2dd0250] /lib/aarch64-linux-gnu/libc.so.6(+0x2229c) [0xffffbd9d229c] This is a test 0.000 s: test explicit logger 01:46:38.557 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.557 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.558 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.008 s: gvcf iterator 01:46:38.566 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.566 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.566 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.009 s: columnar_gvcf_iterator_test 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f [TileDB] Error: No TileDB support for URL=dfdfd://ddd. 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 htslib_plugin could not open dfdfd://ddd No TileDB support for URL=dfdfd://ddd 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f/foo 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin could not find /tmp/GenomicsDBmtop7f/foo [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin write /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory) [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) 01:46:38.575 ERROR NativeGenomicsDB - pid=854531 tid=854531 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) 0.000 s: test htslib plugin 0.000 s: alleles_combiner 0.000 s: gt_remapper ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ctests is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- test bgen ------------------------------------------------------------------------------- ./src/test/cpp/src/test_bgen.cc:11 ............................................................................... ./src/test/cpp/src/test_bgen.cc:11: FAILED: due to unexpected exception with message: Direct - first BGEN test output did not match reference output 0.000 s: test bgen 01:46:38.640 ERROR NativeGenomicsDB - pid=854531 tid=854531 VariantStorageManagerException exception : Could not open workspace 01:46:38.641 ERROR NativeGenomicsDB - pid=854531 tid=854531 Could not open array non_existent_array in workspace /tmp/GenomicsDBrgMhiQ/ws 01:46:38.641 ERROR NativeGenomicsDB - pid=854531 tid=854531 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDBrgMhiQ/ws 0.000 s: constructor 01:46:38.641 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.641 WARN NativeGenomicsDB - pid=854531 tid=854531 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.642 DEBUG NativeGenomicsDB - pid=854531 tid=854531 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.645 ERROR NativeGenomicsDB - pid=854531 tid=854531 Invalid query attribute : non_existent_attribute 0.005 s: test basic queries 01:46:38.646 INFO NativeGenomicsDB - pid=854531 tid=854531 Mem usage Check basic memory usage rss=46M 0.000 s: check basic memory usage =============================================================================== test cases: 34 | 33 passed | 1 failed assertions: 1440 | 1439 passed | 1 failed 01:46:38.646 DEBUG NativeGenomicsDB - pid=854531 tid=854531 Deleting htslib_fs_adapter tiledb_ctx_map 21: 0.014 s: api query_variant_calls direct DP and GT 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0|0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 0.015 s: api query_variant_calls direct DP and GT with PP 21: 01:46:38.675 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.675 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.675 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] DP:76 21: 01:46:38.680 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.680 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.680 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.684 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.010 s: api query_variant_calls with json 21: 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.684 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.685 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.685 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.690 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.690 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.690 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.691 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.691 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.691 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.691 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.695 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.695 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.696 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.696 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.005 s: Try query with contig intervals instead of tiledb column intervals 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.700 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.700 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.700 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.701 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.701 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.701 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.701 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.711 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.005 s: Try query with a filter 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.716 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.716 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.716 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.717 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.717 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.717 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.717 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.721 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.721 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.722 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.722 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.727 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.727 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.728 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.728 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with a filter and workspace with GT ploidy 21: 0.015 s: api query_variant_calls with protobuf 21: 01:46:38.731 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.731 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.731 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.732 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.732 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.732 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.732 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.737 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.737 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.738 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.738 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.743 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.743 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.744 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.744 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with a filter and a small segment size to force TileDB buffers overflow 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.747 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.747 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.747 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.748 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.748 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.748 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.748 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.752 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.752 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.753 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.753 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.758 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.758 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.759 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.759 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with POS and ROW with no match 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.763 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.763 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.763 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.764 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.764 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.764 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.764 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.774 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.774 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.774 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.775 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.775 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.775 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.775 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with POS and ROW 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.778 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.778 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.779 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.779 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.780 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.780 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.780 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.785 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.785 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.786 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.786 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.790 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.790 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.790 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.791 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.791 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.791 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.791 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with ISHOMREF 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.794 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.794 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.794 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.795 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.795 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.796 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.796 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.800 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.800 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.801 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.801 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.806 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.806 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.807 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.807 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with ISHOMREF 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.810 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.810 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.810 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.811 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.811 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.811 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.811 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.815 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.004 s: Try query with ISHOMREF 21: 0.016 s: api query_variant_calls with protobuf 21: 01:46:38.826 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.826 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.826 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.827 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.827 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.827 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.827 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.832 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.832 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.832 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.833 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.833 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.833 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.833 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: sample=HG00141 21: row=0 position=12140 21: genomic_interval=1:12141,12295 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG01958 21: row=1 position=12144 21: genomic_interval=1:12145,12277 21: genomic_fields 21: REF:C ALT:[] GT:0/0 21: sample=HG00141 21: row=0 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 21: sample=HG01958 21: row=1 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[T, ] GT:1/1 DP:120 21: sample=HG01530 21: row=2 position=17384 21: genomic_interval=1:17385,17385 21: genomic_fields 21: REF:G ALT:[A, ] GT:0/1 DP:76 21: 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.005 s: Try query with ISHOMREF 21: 0.017 s: api query_variant_calls with protobuf 21: 0.002 s: Base configuration 21: 0.003 s: api query_variant_calls with protobuf and config 21: 01:46:38.846 ERROR NativeGenomicsDB - pid=854532 tid=854532 Could not parse query_configuration. Only protobuf QueryConfiguration binary strings accepted as input argument 21: 0.000 s: Subset Array with pb string that is not Query or ExportConfiguration 21: 0.001 s: api query_variant_calls with protobuf and config 21: 0.002 s: Subset Array using QueryConfiguration 21: 0.003 s: api query_variant_calls with protobuf and config 21: 0.002 s: Subset Array using ExportConfiguration 21: 0.003 s: api query_variant_calls with protobuf and config 21: 0.003 s: Subset Array using QueryConfiguration - two intervals 21: 0.004 s: api query_variant_calls with protobuf and config 21: 0.003 s: Subset Array using QueryConfiguration - multiple queries 21: 0.004 s: api query_variant_calls with protobuf and config 21: 0.003 s: Test filter test for 0 21: 0.003 s: api query_variant_calls with protobuf new 21: 0.003 s: Test filter test for 1 21: 0.003 s: api query_variant_calls with protobuf new 21: 0.003 s: Test filter test for 2 21: 0.003 s: api query_variant_calls with protobuf new 21: 0.003 s: Test filter test for 3 21: 0.003 s: api query_variant_calls with protobuf new 21: 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"DP":[null,null],"GT":["C/C","G/A"],"REF":["C","G"]},"HG01530":{"CHR":["1"],"POS":[17385],"DP":[76],"GT":["G/A"],"REF":["G"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"DP":[null,120],"GT":["C/C","T/T"],"REF":["C","G"]}} 21: 21: 207 {"FIELD":["CHR","POS","DP","GT","REF"],"HG00141":[["1",12141,null,"C/C","C"],["1",17385,null,"G/A","G"]],"HG01530":[["1",17385,76,"G/A","G"]],"HG01958":[["1",12145,null,"C/C","C"],["1",17385,120,"T/T","G"]]} 21: 21: 37 {"HG00141":2,"HG01530":1,"HG01958":2} 21: 21: 15 {"num_calls":5} 21: 21: 15 {"num_calls":5} 21: 21: 31 ["HG00141","HG01530","HG01958"] 21: 21: 21: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 21: api_tests is a Catch2 v3.7.1 host application. 21: Run with -? for options 21: 21: ------------------------------------------------------------------------------- 21: api query_variant_calls with JSONVariantCallProcessor 21: ------------------------------------------------------------------------------- 21: ./src/test/cpp/src/test_genomicsdb_api.cc:887 21: ............................................................................... 21: 21: ./src/test/cpp/src/test_genomicsdb_api.cc:997: FAILED: 21: CHECK( output.length() == 1805 ) 21: with expansion: 21: 1807 (0x70f) == 1805 (0x70d) 21: 21: 1807 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"AD":[null,58],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DP":[null,null],"DP_FORMAT":[2,80],"DS":["1","1"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","G/A"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,1],"MLEAF":[null,0.5],"MQ":[null,31.719999313354493],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"PL":[0,504],"QUAL":[null,475.7699890136719],"RAW_MQ":[null,5.5],"REF":["C","G"],"ReadPosRankSum":[null,0.004999999888241291],"SB":[null,"[58, 0, 22, 0]"]},"HG01530":{"CHR":["1"],"POS":[17385],"AD":[40],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DP":[76],"DP_FORMAT":[76],"DS":["127"],"FILTER":[null],"GQ":[99],"GT":["G/A"],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MIN_DP":[null],"MLEAC":[1],"MLEAF":[0.5],"MQ":[59.369998931884769],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"PGT":[null],"PID":[null],"PL":[1018],"QUAL":[989.77001953125],"RAW_MQ":[null],"REF":["G"],"ReadPosRankSum":[2.055000066757202],"SB":["[9, 31, 13, 23]"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"AD":[null,0],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DP":[null,120],"DP_FORMAT":[3,120],"DS":["1","127"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","T/T"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,2],"MLEAF":[null,1.0],"MQ":[null,29.81999969482422],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"PL":[0,3336],"QUAL":[null,3302.77001953125],"RAW_MQ":[null,2.5],"REF":["C","G"],"ReadPosRankSum":[null,-0.10100000351667404],"SB":[null,"[0, 0, 0, 0]"]}} 21: 21: 0.021 s: api query_variant_calls with JSONVariantCallProcessor 21: 0.000 s: Test genomicsdb demo test case 21: 0.014 s: api generate_vcf direct 21: 01:46:38.910 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.910 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.910 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 9: =============================================================================== 9: All tests passed (10488234 assertions in 9 test cases) 9: 21: 0.006 s: api generate_vcf with json 21: 01:46:38.916 DEBUG NativeGenomicsDB - pid=854532 tid=854684 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.916 WARN NativeGenomicsDB - pid=854532 tid=854684 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.916 DEBUG NativeGenomicsDB - pid=854532 tid=854684 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 16/22 Test #9: test_tiledb_utils ................ Passed 0.52 sec 21: 01:46:38.917 DEBUG NativeGenomicsDB - pid=854532 tid=854685 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854685 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854683 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854683 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854686 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854686 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854688 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854688 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854685 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.919 DEBUG NativeGenomicsDB - pid=854532 tid=854683 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.919 DEBUG NativeGenomicsDB - pid=854532 tid=854682 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.919 WARN NativeGenomicsDB - pid=854532 tid=854682 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854689 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.920 WARN NativeGenomicsDB - pid=854532 tid=854689 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854682 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854686 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854688 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854689 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.923 DEBUG NativeGenomicsDB - pid=854532 tid=854687 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.923 WARN NativeGenomicsDB - pid=854532 tid=854687 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.924 DEBUG NativeGenomicsDB - pid=854532 tid=854687 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.035 s: api generate_vcf with json multiple threads 21: 01:46:38.951 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.951 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.951 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.952 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.952 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.952 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.952 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.956 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.956 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.957 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.957 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.961 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 21: 01:46:38.961 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.961 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.962 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 01:46:38.962 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 01:46:38.962 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 21: 01:46:38.962 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: ---------------- 21: Interval:[0,1000000000] 21: 21: ---------------- 21: Interval:[0,1000000000] 21: 21: 0.014 s: api annotate query_variant_calls with test datasource 0 21: =============================================================================== 21: test cases: 26 | 25 passed | 1 failed 21: assertions: 1531 | 1530 passed | 1 failed 21: 22: 01:46:38.925 INFO NativeGenomicsDB - pid=854681 tid=854681 Reading 1 vcfs 22: 01:46:38.928 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 1 / 3] Reading 1 / 1 = 100.00% 22: 01:46:38.957 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 2 / 3] read_next_batch 0 / 1 = 0.00% 22: 01:46:38.958 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 3 / 3] progress: 12140 / 249250620 = 0.00% 22: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR 22: [TileDB::Codec] Error: Could not compress with GZIP. 22: [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/1$1$249250621/.__aec1b05c-bdf0-4a86-b601-cd965295a162281473598140448_1745588798941/END.tdb. 22: 01:46:38.959 ERROR NativeGenomicsDB - pid=854681 tid=854681 VariantStorageManagerException exception : Error while finalizing GenomicsDB array 1$1$249250621 : [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/1$1$249250621/.__aec1b05c-bdf0-4a86-b601-cd965295a162281473598140448_1745588798941/END.tdb 17/22 Test #21: api_tests ........................***Failed 0.49 sec Randomness seeded to: 1906762867 0.001 s: utils 0.000 s: api empty_args 0.021 s: api query_variants direct DP 0.007 s: api query_variants direct DP with huge row range 0.006 s: api query_variants direct DP with huge disjoint row ranges 0.011 s: api query_variants direct DP with range composed of multiple points 0.009 s: api query_variants direct DP with range composed of overlapping ranges 01:46:38.575 ERROR NativeGenomicsDB - pid=854532 tid=854532 Query interval 0:-100-1 is out of bounds 0.003 s: api query_variants direct DP with invalid row range 0.013 s: api query_variants direct DP and GT 0.012 s: api query_variants direct DP and GT with PP 01:46:38.602 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.602 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.602 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.608 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.608 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.608 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.613 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.613 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.613 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.012 s: api query_variants with json 01:46:38.614 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.614 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.614 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock 01:46:38.619 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.619 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.620 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.625 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.012 s: api query variants with json string 01:46:38.625 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.626 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.626 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.005 s: api query variants with enabled shared posixfs optimizations ---------------- Interval:[0,9223372036854775806] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] DP:76 ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] DP:76 0.015 s: api query_variant_calls direct ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 0.014 s: api query_variant_calls direct DP and GT ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0|0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 0.015 s: api query_variant_calls direct DP and GT with PP 01:46:38.675 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.675 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.675 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] DP:76 01:46:38.680 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.680 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.680 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.684 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.010 s: api query_variant_calls with json 01:46:38.684 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.684 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.685 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.685 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.685 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.690 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.690 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.690 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.691 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.691 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.691 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.691 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.695 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.695 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.696 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.696 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.696 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.005 s: Try query with contig intervals instead of tiledb column intervals 0.016 s: api query_variant_calls with protobuf 01:46:38.700 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.700 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.700 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.701 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.701 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.701 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.701 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.706 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.706 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.711 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.712 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.712 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.005 s: Try query with a filter 0.016 s: api query_variant_calls with protobuf 01:46:38.716 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.716 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.716 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.717 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.717 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.717 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.717 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.721 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.721 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.722 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.722 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.722 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.727 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.727 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.728 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.728 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.728 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with a filter and workspace with GT ploidy 0.015 s: api query_variant_calls with protobuf 01:46:38.731 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.731 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.731 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.732 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.732 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.732 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.732 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.737 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.737 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.737 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.738 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.738 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.743 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.743 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.743 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.744 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.744 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with a filter and a small segment size to force TileDB buffers overflow 0.016 s: api query_variant_calls with protobuf 01:46:38.747 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.747 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.747 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.748 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.748 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.748 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.748 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.752 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.752 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.753 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.753 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.753 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.758 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.758 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.759 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.759 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.759 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with POS and ROW with no match 0.016 s: api query_variant_calls with protobuf 01:46:38.763 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.763 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.763 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.764 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.764 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.764 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.764 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.769 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.769 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.774 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.774 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.774 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.775 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.775 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.775 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.775 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with POS and ROW 0.016 s: api query_variant_calls with protobuf 01:46:38.778 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.778 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.779 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.779 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.780 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.780 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.780 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.785 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.785 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.785 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.786 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.786 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.790 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.790 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.790 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.791 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.791 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.791 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.791 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with ISHOMREF 0.016 s: api query_variant_calls with protobuf 01:46:38.794 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.794 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.794 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.795 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.795 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.796 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.796 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.800 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.800 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.801 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.801 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.801 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.806 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.806 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.806 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.807 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.807 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with ISHOMREF 0.016 s: api query_variant_calls with protobuf 01:46:38.810 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.810 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.810 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.811 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.811 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.811 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.811 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.815 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.816 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.816 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.822 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.822 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.004 s: Try query with ISHOMREF 0.016 s: api query_variant_calls with protobuf 01:46:38.826 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.826 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.826 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.827 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.827 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.827 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.827 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.832 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.832 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.832 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.833 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.833 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.833 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.833 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] sample=HG00141 row=0 position=12140 genomic_interval=1:12141,12295 genomic_fields REF:C ALT:[] GT:0/0 sample=HG01958 row=1 position=12144 genomic_interval=1:12145,12277 genomic_fields REF:C ALT:[] GT:0/0 sample=HG00141 row=0 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 sample=HG01958 row=1 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[T, ] GT:1/1 DP:120 sample=HG01530 row=2 position=17384 genomic_interval=1:17385,17385 genomic_fields REF:G ALT:[A, ] GT:0/1 DP:76 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.838 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.838 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.005 s: Try query with ISHOMREF 0.017 s: api query_variant_calls with protobuf 0.002 s: Base configuration 0.003 s: api query_variant_calls with protobuf and config 01:46:38.846 ERROR NativeGenomicsDB - pid=854532 tid=854532 Could not parse query_configuration. Only protobuf QueryConfiguration binary strings accepted as input argument 0.000 s: Subset Array with pb string that is not Query or ExportConfiguration 0.001 s: api query_variant_calls with protobuf and config 0.002 s: Subset Array using QueryConfiguration 0.003 s: api query_variant_calls with protobuf and config 0.002 s: Subset Array using ExportConfiguration 0.003 s: api query_variant_calls with protobuf and config 0.003 s: Subset Array using QueryConfiguration - two intervals 0.004 s: api query_variant_calls with protobuf and config 0.003 s: Subset Array using QueryConfiguration - multiple queries 0.004 s: api query_variant_calls with protobuf and config 0.003 s: Test filter test for 0 0.003 s: api query_variant_calls with protobuf new 0.003 s: Test filter test for 1 0.003 s: api query_variant_calls with protobuf new 0.003 s: Test filter test for 2 0.003 s: api query_variant_calls with protobuf new 0.003 s: Test filter test for 3 0.003 s: api query_variant_calls with protobuf new 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"DP":[null,null],"GT":["C/C","G/A"],"REF":["C","G"]},"HG01530":{"CHR":["1"],"POS":[17385],"DP":[76],"GT":["G/A"],"REF":["G"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"DP":[null,120],"GT":["C/C","T/T"],"REF":["C","G"]}} 207 {"FIELD":["CHR","POS","DP","GT","REF"],"HG00141":[["1",12141,null,"C/C","C"],["1",17385,null,"G/A","G"]],"HG01530":[["1",17385,76,"G/A","G"]],"HG01958":[["1",12145,null,"C/C","C"],["1",17385,120,"T/T","G"]]} 37 {"HG00141":2,"HG01530":1,"HG01958":2} 15 {"num_calls":5} 15 {"num_calls":5} 31 ["HG00141","HG01530","HG01958"] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api_tests is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- api query_variant_calls with JSONVariantCallProcessor ------------------------------------------------------------------------------- ./src/test/cpp/src/test_genomicsdb_api.cc:887 ............................................................................... ./src/test/cpp/src/test_genomicsdb_api.cc:997: FAILED: CHECK( output.length() == 1805 ) with expansion: 1807 (0x70f) == 1805 (0x70d) 1807 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"AD":[null,58],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DP":[null,null],"DP_FORMAT":[2,80],"DS":["1","1"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","G/A"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,1],"MLEAF":[null,0.5],"MQ":[null,31.719999313354493],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"PL":[0,504],"QUAL":[null,475.7699890136719],"RAW_MQ":[null,5.5],"REF":["C","G"],"ReadPosRankSum":[null,0.004999999888241291],"SB":[null,"[58, 0, 22, 0]"]},"HG01530":{"CHR":["1"],"POS":[17385],"AD":[40],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DP":[76],"DP_FORMAT":[76],"DS":["127"],"FILTER":[null],"GQ":[99],"GT":["G/A"],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MIN_DP":[null],"MLEAC":[1],"MLEAF":[0.5],"MQ":[59.369998931884769],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"PGT":[null],"PID":[null],"PL":[1018],"QUAL":[989.77001953125],"RAW_MQ":[null],"REF":["G"],"ReadPosRankSum":[2.055000066757202],"SB":["[9, 31, 13, 23]"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"AD":[null,0],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DP":[null,120],"DP_FORMAT":[3,120],"DS":["1","127"],"FILTER":[null,0],"GQ":[0,99],"GT":["C/C","T/T"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MIN_DP":[0,null],"MLEAC":[null,2],"MLEAF":[null,1.0],"MQ":[null,29.81999969482422],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"PL":[0,3336],"QUAL":[null,3302.77001953125],"RAW_MQ":[null,2.5],"REF":["C","G"],"ReadPosRankSum":[null,-0.10100000351667404],"SB":[null,"[0, 0, 0, 0]"]}} 0.021 s: api query_variant_calls with JSONVariantCallProcessor 0.000 s: Test genomicsdb demo test case 0.014 s: api generate_vcf direct 01:46:38.910 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.910 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.910 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.006 s: api generate_vcf with json 01:46:38.916 DEBUG NativeGenomicsDB - pid=854532 tid=854684 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.916 WARN NativeGenomicsDB - pid=854532 tid=854684 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.916 DEBUG NativeGenomicsDB - pid=854532 tid=854684 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.917 DEBUG NativeGenomicsDB - pid=854532 tid=854685 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854685 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854683 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854683 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854686 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854686 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854688 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.918 WARN NativeGenomicsDB - pid=854532 tid=854688 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.918 DEBUG NativeGenomicsDB - pid=854532 tid=854685 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.919 DEBUG NativeGenomicsDB - pid=854532 tid=854683 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.919 DEBUG NativeGenomicsDB - pid=854532 tid=854682 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.919 WARN NativeGenomicsDB - pid=854532 tid=854682 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854689 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.920 WARN NativeGenomicsDB - pid=854532 tid=854689 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854682 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854686 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854688 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.920 DEBUG NativeGenomicsDB - pid=854532 tid=854689 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.923 DEBUG NativeGenomicsDB - pid=854532 tid=854687 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.923 WARN NativeGenomicsDB - pid=854532 tid=854687 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.924 DEBUG NativeGenomicsDB - pid=854532 tid=854687 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.035 s: api generate_vcf with json multiple threads 01:46:38.951 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.951 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.951 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.952 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.952 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.952 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.952 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.956 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.956 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.957 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.957 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.957 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.961 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn 01:46:38.961 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.961 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.962 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 01:46:38.962 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 01:46:38.962 DEBUG NativeGenomicsDB - pid=854532 tid=854532 json file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(callsets): missing field sample_name 01:46:38.962 WARN NativeGenomicsDB - pid=854532 tid=854532 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead ---------------- Interval:[0,1000000000] ---------------- Interval:[0,1000000000] 0.014 s: api annotate query_variant_calls with test datasource 0 =============================================================================== test cases: 26 | 25 passed | 1 failed assertions: 1531 | 1530 passed | 1 failed 22: command 'vcf2genomicsdb --progress /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/loader.json' returned 139 unexpectedly 18/22 Test #22: tools_tests ......................***Failed 0.48 sec 01:46:38.925 INFO NativeGenomicsDB - pid=854681 tid=854681 Reading 1 vcfs 01:46:38.928 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 1 / 3] Reading 1 / 1 = 100.00% 01:46:38.957 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 2 / 3] read_next_batch 0 / 1 = 0.00% 01:46:38.958 INFO NativeGenomicsDB - pid=854681 tid=854681 [STAGE 3 / 3] progress: 12140 / 249250620 = 0.00% [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR [TileDB::Codec] Error: Could not compress with GZIP. [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/1$1$249250621/.__aec1b05c-bdf0-4a86-b601-cd965295a162281473598140448_1745588798941/END.tdb. 01:46:38.959 ERROR NativeGenomicsDB - pid=854681 tid=854681 VariantStorageManagerException exception : Error while finalizing GenomicsDB array 1$1$249250621 : [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/1$1$249250621/.__aec1b05c-bdf0-4a86-b601-cd965295a162281473598140448_1745588798941/END.tdb command 'vcf2genomicsdb --progress /tmp/test_tools-GenomicsDB-7Xsuy42sBc/ws_10744/loader.json' returned 139 unexpectedly 7: Randomness seeded to: 4222664589 14: Fri Apr 25 01:46:39 2025 Memory stats Tracking memory usage END size=6MB resident=1MB share=1MB text=604KB lib=0 data=540KB dt=0 14: =============================================================================== 14: test cases: 1 | 1 passed 14: assertions: - none - 14: 19/22 Test #14: test_mem_utils ................... Passed 1.01 sec 18: =============================================================================== 18: All tests passed (450703 assertions in 3 test cases) 18: 20/22 Test #18: test_storage_buffer .............. Passed 1.20 sec 8: Randomness seeded to: 3798153578 8: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== 8: All tests passed (10501238 assertions in 15 test cases) 8: 21/22 Test #8: test_sparse_array_api ............ Passed 2.56 sec 7: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== 7: All tests passed (96999771 assertions in 4 test cases) 7: 22/22 Test #7: test_dense_array_api ............. Passed 3.42 sec 73% tests passed, 6 tests failed out of 22 Total Test time (real) = 3.44 sec The following tests FAILED: 5 - test_array_iterator (SEGFAULT) 6 - test_array_schema_api (Failed) 19 - ci_tests (Failed) 20 - ctests (Failed) 21 - api_tests (Failed) 22 - tools_tests (Failed) Errors while running CTest make[2]: *** [Makefile:74: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' dh_auto_test: error: cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/genomicsdb-1.5.4 -B/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/depend make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/depend make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/build Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/protobuf_ep.dir/build'. Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". [ 0%] Built target protobuf_ep Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_buffer.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/resources /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target genomicsdb-hts make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target TILEDB_CORE_OBJECTS make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build [ 13%] Built target genomicsdb-hts [ 13%] Built target PROTOBUF_GENERATED_CXX_TARGET make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". [ 25%] Built target TILEDB_CORE_OBJECTS Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake "--color=" Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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[ 25%] Built target tiledb_static [ 26%] Built target tiledb_shared make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 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'/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test 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"/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake "--color=" make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_print_array_schema Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_array_iterator Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_array_schema Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_print_book_keeping make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_array_schema_api Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_dense_array_api Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_tiledb_utils make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_sparse_array_api Consolidate compiler generated dependencies of target test_sparse_array_benchmark make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build Consolidate compiler generated dependencies of target test_codec make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 27%] Built target test_print_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build [ 27%] Built target test_print_book_keeping [ 28%] Built target test_array_iterator [ 29%] Built target test_sparse_array_benchmark [ 29%] Built target test_array_schema [ 44%] Built target GenomicsDB_library_object_files make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend [ 45%] Built target test_array_schema_api make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake "--color=" [ 47%] Built target test_sparse_array_api [ 47%] Built target test_dense_array_api make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/depend make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/depend [ 48%] Built target test_tiledb_utils cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/compiler_depend.internal". [ 49%] Built target test_codec Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend Consolidate compiler generated dependencies of target test_codec_filter make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_uri Consolidate compiler generated dependencies of target test_mem_utils make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_expressions make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_utils Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_3d make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/compiler_depend.internal". 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Consolidate compiler generated dependencies of target test_filter_api Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_storage_buffer Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_aio_read_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target test_posixfs make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 49%] Built target test_codec_filter make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 49%] Built target test_uri [ 49%] Built target test_mem_utils [ 50%] Built target test_utils [ 50%] Built target test_expressions make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake "--color=" [ 51%] Built target test_filter_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples 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[ 52%] Built target tiledb_array_aio_read_dense Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_aio_write_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake "--color=" [ 53%] Built target test_posixfs make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_consolidate Consolidate compiler generated dependencies of target tiledb_array_create_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_create_sparse make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 54%] Built target tiledb_array_aio_write_dense [ 55%] Built target tiledb_array_consolidate Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_iterator_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake "--color=" [ 55%] Built target tiledb_array_create_dense Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse_filter make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/depend [ 56%] Built target tiledb_array_create_sparse Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". [ 57%] Built target tiledb_array_iterator_sparse Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_sparse [ 58%] Built target tiledb_array_iterator_sparse_filter make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 58%] Built target tiledb_array_iterator_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake "--color=" [ 58%] Built target tiledb_array_parallel_consolidate_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_2 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/src/tiledb_array_parallel_read_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/compiler_depend.internal". [ 59%] Built target tiledb_array_parallel_consolidate_sparse Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/src/tiledb_array_parallel_write_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_1 Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_parallel_read_mpi_io_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/src/tiledb_array_parallel_write_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_1 Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_2 Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 60%] Built target tiledb_array_parallel_read_dense_2 [ 60%] Built target tiledb_array_parallel_read_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build'. make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 60%] Built target tiledb_array_parallel_read_sparse_1 [ 61%] Built target tiledb_array_parallel_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend [ 62%] Built target tiledb_array_parallel_write_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake "--color=" [ 63%] Built target tiledb_array_parallel_read_mpi_io_dense [ 63%] Built target tiledb_array_parallel_write_sparse_2 [ 63%] Built target tiledb_array_parallel_write_dense_2 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/compiler_depend.internal". [ 64%] Built target tiledb_array_parallel_write_sparse_1 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_primitive make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_1 Consolidate compiler generated dependencies of target tiledb_array_read_dense_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_3 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_dense_sorted make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". [ 65%] Built target tiledb_array_primitive Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_sparse_1 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_sparse_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_1 [ 66%] Built target tiledb_array_read_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 67%] Built target tiledb_array_read_dense_3 [ 67%] Built target tiledb_array_read_dense_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend [ 68%] Built target tiledb_array_read_dense_sorted Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 68%] Built target tiledb_array_read_sparse_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend [ 69%] Built target tiledb_array_read_sparse_filter_1 [ 69%] Built target tiledb_array_read_sparse_2 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_sparse_sorted make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_update_dense_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_update_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_update_dense_2 Consolidate compiler generated dependencies of target tiledb_array_update_sparse_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/depend Consolidate compiler generated dependencies of target tiledb_array_write_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake "--color=" [ 70%] Built target tiledb_array_read_sparse_filter_2 [ 71%] Built target tiledb_array_read_sparse_sorted make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 73%] Built target tiledb_array_update_dense_2 [ 73%] Built target tiledb_array_update_sparse_2 [ 73%] Built target tiledb_array_update_dense_1 [ 73%] Built target tiledb_array_update_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/compiler_depend.internal". cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend Consolidate compiler generated dependencies of target tiledb_array_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_write_dense_sorted [ 74%] Built target tiledb_array_write_dense_1 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_config Consolidate compiler generated dependencies of target tiledb_array_write_sparse_4 Consolidate compiler generated dependencies of target tiledb_clear_delete_move make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". [ 74%] Built target tiledb_array_write_dense_2 Consolidate compiler generated dependencies of target tiledb_array_write_sparse_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_ls make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_sparse_3 Consolidate compiler generated dependencies of target tiledb_delete make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build [ 75%] Built target tiledb_array_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build Consolidate compiler generated dependencies of target tiledb_catching_errors make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_ls_workspaces make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 75%] Built target tiledb_array_write_sparse_4 [ 75%] Built target tiledb_array_write_sparse_2 [ 76%] Built target tiledb_clear_delete_move [ 76%] Built target tiledb_config [ 78%] Built target tiledb_array_write_dense_sorted [ 78%] Built target tiledb_catching_errors make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend [ 79%] Built target tiledb_ls make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake "--color=" [ 80%] Built target tiledb_delete make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend [ 81%] Built target tiledb_array_write_sparse_3 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake "--color=" make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake "--color=" [ 81%] Built target tiledb_ls_workspaces Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_metadata_consolidate Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_create make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_metadata_iterator Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend Consolidate compiler generated dependencies of target tiledb_metadata_primitive Consolidate compiler generated dependencies of target tiledb_metadata_read make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_update make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_workspace_group_create Consolidate compiler generated dependencies of target tiledb_metadata_write make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build'. make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 82%] Built target tiledb_metadata_consolidate [ 82%] Built target tiledb_metadata_create Dependencies file "src/main/CMakeFiles/tiledbgenomicsdb.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledbgenomicsdb make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdb.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build [ 84%] Built target tiledb_metadata_update [ 85%] Built target tiledb_metadata_read [ 84%] Built target tiledb_metadata_write [ 84%] Built target tiledb_metadata_primitive [ 85%] Built target tiledb_metadata_iterator make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/tiledbgenomicsdb.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 86%] Built target tiledb_workspace_group_create [ 86%] Built target genomicsdb make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/depend make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/DependInfo.cmake "--color=" make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake "--color=" make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake "--color=" make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/DependInfo.cmake "--color=" make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake "--color=" [ 86%] Built target tiledbgenomicsdb make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake "--color=" Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/src/test_genomicsdb_demo.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend Dependencies file "tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/gt_mpi_gather.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake "--color=" Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_genomicsdb_demo Consolidate compiler generated dependencies of target vcf2genomicsdb Dependencies file "tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf2genomicsdb_init.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target gt_mpi_gather Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/build Consolidate compiler generated dependencies of target api_tests Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build Consolidate compiler generated dependencies of target vcf_histogram Consolidate compiler generated dependencies of target vcf2genomicsdb_init Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_mem_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_query_variants.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/gt_mpi_gather.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target consolidate_genomicsdb_array Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/api_tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build Consolidate compiler generated dependencies of target create_genomicsdb_workspace Dependencies file "tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". 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Dependencies file "example/CMakeFiles/test_genomicsdb_bcf_generator.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/consolidate_genomicsdb_array.dir/build'. make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf_histogram.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb_init.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target vcfdiff Consolidate compiler generated dependencies of target test_genomicsdb_importer Consolidate compiler generated dependencies of target test_genomicsdb_bcf_generator make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/create_genomicsdb_workspace.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcfdiff.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_importer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' Consolidate compiler generated dependencies of target ctests [ 87%] Built target vcf2genomicsdb [ 87%] Built target test_genomicsdb_demo make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 88%] Built target api_tests [ 89%] Built target gt_mpi_gather make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend [ 89%] Built target vcf2genomicsdb_init [ 90%] Built target consolidate_genomicsdb_array [ 91%] Built target vcfdiff make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.4 /build/reproducible-path/genomicsdb-1.5.4/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake "--color=" [ 92%] Built target vcf_histogram [ 92%] Built target create_genomicsdb_workspace make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/ctests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [ 93%] Built target test_genomicsdb_bcf_generator [ 94%] Built target test_genomicsdb_importer Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". [ 99%] Built target ctests Consolidate compiler generated dependencies of target genomicsdbjni make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdbjni.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' [100%] Built target genomicsdbjni make[3]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu' # Testing the Java part. We extend LD_LIBRARY_PATH because some test code is # run without surefire. LD_LIBRARY_PATH=":obj-aarch64-linux-gnu/src/main" dh_auto_test --buildsystem=maven /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/genomicsdb-1.5.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.4/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.4/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [INFO] [INFO] ---------------------< org.genomicsdb:genomicsdb >---------------------- [INFO] Building org.genomicsdb:genomicsdb 1.5.4 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact com.googlecode.json-simple:json-simple:jar:debian has been relocated to com.github.cliftonlabs:json-simple:jar:debian [INFO] [INFO] --- antrun:3.1.0:run (exec-protoc) @ genomicsdb --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- build-helper:3.3.0:add-source (add-source) @ genomicsdb --- [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.4/src/main/scala added. [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.4/src/main/resources [INFO] [INFO] --- compiler:3.13.0:compile (default-compile) @ genomicsdb --- [INFO] Recompiling the module because of changed source code. [INFO] Compiling 30 source files with javac [debug target 17] to build/classes [WARNING] system modules path not set in conjunction with -source 17 [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java:[37,14] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[79,39] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[206,31] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[483,84] PARSER in org.genomicsdb.model.Coordinates.GenomicsDBColumnOrInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[5485,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[4407,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[10171,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7553,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7594,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7635,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[792,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[3035,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/Coordinates.java:[3987,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBVidMapProto.java:[93,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBCallsetsMapProto.java:[139,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[177,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[2228,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/build/src/main/java/org/genomicsdb/model/GenomicsDBImportConfiguration.java:[2269,30] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/exception/GenomicsDBException.java:[28,8] serializable class org.genomicsdb.exception.GenomicsDBException has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[50,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.Pair has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[70,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.VariantCall has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[76,25] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[110,17] serializable class org.genomicsdb.reader.GenomicsDBQuery.Interval has no definition of serialVersionUID [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[112,23] non-transient instance field of a serializable class declared with a non-serializable type [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/ImportConfig.java:[76,36] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[91,50] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[160,28] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[322,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[333,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[333,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[334,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[334,30] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[336,9] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[336,41] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[338,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[338,36] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[342,17] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[342,40] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[367,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[462,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[462,45] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[483,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[483,41] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[690,94] found raw type: java.util.concurrent.CompletableFuture missing type arguments for generic class java.util.concurrent.CompletableFuture [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[799,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[224,46] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[99,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[109,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[54,27] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[139,58] previous possible 'this' escape happens here via invocation [INFO] [INFO] --- antrun:3.1.0:run (copy-native-libs) @ genomicsdb --- [INFO] Executing tasks [WARNING] [exec] The command attribute is deprecated. [exec] Please use the executable attribute and nested arg elements. [INFO] [exec] cp: cannot stat '/build/reproducible-path/genomicsdb-1.5.4/build/src/main/libtiledbgenomicsdb.dylib': No such file or directory [INFO] [exec] Result: 1 [WARNING] [exec] The command attribute is deprecated. [exec] Please use the executable attribute and nested arg elements. [INFO] [exec] cp: cannot stat '/build/reproducible-path/genomicsdb-1.5.4/build/src/main/libtiledbgenomicsdb.so': No such file or directory [INFO] [exec] Result: 1 [INFO] Executed tasks [INFO] [INFO] --- resources:3.3.1:testResources (default-testResources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.4/src/test/resources [INFO] [INFO] --- antrun:3.1.0:run (unzip-test-artifacts) @ genomicsdb --- [INFO] Executing tasks [INFO] [untar] Expanding: /build/reproducible-path/genomicsdb-1.5.4/build/test/test.tar into /build/reproducible-path/genomicsdb-1.5.4/build/test [INFO] Executed tasks [INFO] [INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ genomicsdb --- [INFO] Recompiling the module because of changed dependency. [INFO] Compiling 12 source files with javac [debug target 17] to build/test-classes [WARNING] system modules path not set in conjunction with -source 17 [INFO] Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. [WARNING] No processor claimed any of these annotations: /org.testng.annotations.BeforeClass,/org.testng.annotations.Test,/org.testng.annotations.DataProvider,/org.testng.annotations.BeforeMethod,/org.testng.annotations.AfterMethod [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,38] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,13] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,39] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,44] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[201,18] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[257,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[289,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[322,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[362,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[398,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[443,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[482,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [WARNING] /build/reproducible-path/genomicsdb-1.5.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[536,9] found raw type: org.genomicsdb.reader.GenomicsDBFeatureReader missing type arguments for generic class org.genomicsdb.reader.GenomicsDBFeatureReader [INFO] [INFO] --- surefire:2.22.3:test (default-test) @ genomicsdb --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB ERROR StatusLogger Reconfiguration failed: No configuration found for '639fee48' at 'null' in 'null' [INFO] [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7.852 s [INFO] Finished at: 2025-04-25T01:46:53-12:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on project genomicsdb: There are test failures. [ERROR] [ERROR] Please refer to /build/reproducible-path/genomicsdb-1.5.4/build/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream. [ERROR] The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd '/build/reproducible-path/genomicsdb-1.5.4' && '/usr/lib/jvm/java-21-openjdk-arm64/bin/java' '-Djava.library.path=:obj-aarch64-linux-gnu/src/main:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main' '-jar' '/build/reproducible-path/genomicsdb-1.5.4/build/surefire/surefirebooter8684513340915118246.jar' '/build/reproducible-path/genomicsdb-1.5.4/build/surefire' '2025-04-25T01-46-51_870-jvmRun1' 'surefire15256884992273463907tmp' 'surefire_08532473975193575272tmp' [ERROR] Error occurred in starting fork, check output in log [ERROR] Process Exit Code: 134 [ERROR] Crashed tests: [ERROR] org.genomicsdb.importer.GenomicsDBImporterSpec [ERROR] org.apache.maven.surefire.booter.SurefireBooterForkException: The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd '/build/reproducible-path/genomicsdb-1.5.4' && '/usr/lib/jvm/java-21-openjdk-arm64/bin/java' '-Djava.library.path=:obj-aarch64-linux-gnu/src/main:/usr/java/packages/lib:/usr/lib/aarch64-linux-gnu/jni:/lib/aarch64-linux-gnu:/usr/lib/aarch64-linux-gnu:/usr/lib/jni:/lib:/usr/lib:/build/reproducible-path/genomicsdb-1.5.4/obj-aarch64-linux-gnu/src/main' '-jar' '/build/reproducible-path/genomicsdb-1.5.4/build/surefire/surefirebooter8684513340915118246.jar' '/build/reproducible-path/genomicsdb-1.5.4/build/surefire' '2025-04-25T01-46-51_870-jvmRun1' 'surefire15256884992273463907tmp' 'surefire_08532473975193575272tmp' [ERROR] Error occurred in starting fork, check output in log [ERROR] Process Exit Code: 134 [ERROR] Crashed tests: [ERROR] org.genomicsdb.importer.GenomicsDBImporterSpec [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:669) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:282) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:245) [ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:1186) [ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:1014) [ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:860) [ERROR] at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:126) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute2(MojoExecutor.java:328) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute(MojoExecutor.java:316) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:174) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.access$000(MojoExecutor.java:75) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor$1.run(MojoExecutor.java:162) [ERROR] at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute(DefaultMojosExecutionStrategy.java:39) [ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:159) [ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:105) [ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:73) [ERROR] at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:53) [ERROR] at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:118) [ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:261) [ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:173) [ERROR] at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:101) [ERROR] at org.apache.maven.cli.MavenCli.execute(MavenCli.java:906) [ERROR] at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:283) [ERROR] at org.apache.maven.cli.MavenCli.main(MavenCli.java:206) [ERROR] at org.apache.maven.cli.MavenCli.main(MavenCli.java:196) [ERROR] at org.debian.maven.Wrapper.main(Wrapper.java:89) [ERROR] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) [ERROR] at java.base/java.lang.reflect.Method.invoke(Method.java:580) [ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:322) [ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:235) [ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:407) [ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:348) [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException dh_auto_test: error: /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/genomicsdb-1.5.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.4/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.4/debian/maven-repo --batch-mode test returned exit code 1 make[1]: *** [debian/rules:68: override_dh_auto_test-indep] Error 25 make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.4' make: *** [debian/rules:14: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/811065 and its subdirectories