I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 14:24:20 +14 2025 I: pbuilder-time-stamp: 1758155060 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_1.5.5-1.dsc] I: copying [./genomicsdb_1.5.5.orig-genomicsdb-htslib.tar.gz] I: copying [./genomicsdb_1.5.5.orig-genomicsdb-tiledb.tar.gz] I: copying [./genomicsdb_1.5.5.orig.tar.gz] I: copying [./genomicsdb_1.5.5-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./genomicsdb_1.5.5-1.dsc: no acceptable signature found dpkg-source: info: extracting genomicsdb in genomicsdb-1.5.5 dpkg-source: info: unpacking genomicsdb_1.5.5.orig.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.5.orig-genomicsdb-htslib.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.5.orig-genomicsdb-tiledb.tar.gz dpkg-source: info: unpacking genomicsdb_1.5.5-1.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/3078223/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 18 00:24 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3078223/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3078223/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=896f25056a1b4ceca12ecba838b2677d LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3078223 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bbem8Wcv/pbuilderrc_Es9H --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bbem8Wcv/b2 --logfile b2/build.log genomicsdb_1.5.5-1.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3078223/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: amd64 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 ... 19917 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-15{a} gfortran-15-x86-64-linux-gnu{a} gpg{a} gpg-agent{a} gpgconf{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} libdrm-intel1{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-15-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} libio-string-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} libksba8{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-reporting-impl-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} 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} libpng16-16t64{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl-dev{a} libpsl5t64{a} libpsm2-2{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} 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} libxml2-16{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} libze1{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} rsopv{a} sensible-utils{a} sgml-base{a} shared-mime-info{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 debian-tag2upload-keyring dput dput-ng dupload equivs fonts-dejavu-extra git-debpush 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 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 libmail-sendmail-perl libmailtools-perl libmetacpan-client-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-debian python3-magic python3-requests python3-unidiff python3-xdg strace systemd-cryptsetup systemd-timesyncd wget xauth xdg-user-dirs 0 packages upgraded, 492 newly installed, 0 to remove and 0 not upgraded. Need to get 457 MB of archives. After unpacking 1560 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libsystemd-shared amd64 258~rc4-1 [2242 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 systemd amd64 258~rc4-1 [3222 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 systemd-sysv amd64 258~rc4-1 [62.7 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 dbus-bin amd64 1.16.2-2 [80.0 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 dbus-session-bus-common all 1.16.2-2 [52.3 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 libapparmor1 amd64 4.1.0-1 [43.7 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 dbus-daemon amd64 1.16.2-2 [159 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 dbus-system-bus-common all 1.16.2-2 [53.5 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 dbus amd64 1.16.2-2 [71.6 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.2-1 [1493 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 ca-certificates all 20250419 [162 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libpam-systemd amd64 258~rc4-1 [314 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 48 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-5 [312 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-5 [141 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 gtk-update-icon-cache amd64 4.20.1+ds-2 [53.4 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 adwaita-icon-theme all 49~rc-1 [507 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 java-common all 0.76 [6776 B] Get: 69 http://deb.debian.org/debian forky/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libnss3 amd64 2:3.114-1 [1399 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libpcsclite1 amd64 2.3.3-1 [55.2 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 openjdk-21-jre-headless amd64 21.0.9~5ea-1 [42.2 MB] Get: 74 http://deb.debian.org/debian forky/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 75 http://deb.debian.org/debian forky/main amd64 ant all 1.10.15-1 [2163 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 at-spi2-common all 2.58.0-1 [173 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 chrpath amd64 0.18-1 [13.5 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 87 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.15.0-1 [392 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 104 http://deb.debian.org/debian forky/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 dbus-user-session amd64 1.16.2-2 [52.1 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libdconf1 amd64 0.40.0-5 [41.8 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 dconf-service amd64 0.40.0-5 [32.4 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 dconf-gsettings-backend amd64 0.40.0-5 [28.6 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 116 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 121 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 libatk1.0-0t64 amd64 2.58.0-1 [57.9 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 126 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 128 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 130 http://deb.debian.org/debian forky/main amd64 libatspi2.0-0t64 amd64 2.58.0-1 [89.8 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libatk-bridge2.0-0t64 amd64 2.58.0-1 [76.4 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 133 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 134 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 135 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 136 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 138 http://deb.debian.org/debian forky/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 139 http://deb.debian.org/debian forky/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 140 http://deb.debian.org/debian forky/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get: 142 http://deb.debian.org/debian forky/main amd64 libcairo-gobject2 amd64 1.18.4-1+b1 [130 kB] Get: 143 http://deb.debian.org/debian forky/main amd64 libcloudproviders0 amd64 0.3.6-2 [29.2 kB] Get: 144 http://deb.debian.org/debian forky/main amd64 libcolord2 amd64 1.4.8-1 [152 kB] Get: 145 http://deb.debian.org/debian forky/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 146 http://deb.debian.org/debian forky/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 147 http://deb.debian.org/debian forky/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 148 http://deb.debian.org/debian forky/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 149 http://deb.debian.org/debian forky/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 150 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 151 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-3 [75.1 kB] Get: 152 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 11.4.5-1 [505 kB] Get: 153 http://deb.debian.org/debian forky/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get: 154 http://deb.debian.org/debian forky/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 155 http://deb.debian.org/debian forky/main amd64 libdatrie1 amd64 0.2.13-4 [38.0 kB] Get: 156 http://deb.debian.org/debian forky/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 157 http://deb.debian.org/debian forky/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] Get: 158 http://deb.debian.org/debian forky/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [62.0 kB] Get: 159 http://deb.debian.org/debian forky/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [38.1 kB] Get: 160 http://deb.debian.org/debian forky/main amd64 libwayland-client0 amd64 1.24.0-2+b1 [28.5 kB] Get: 161 http://deb.debian.org/debian forky/main amd64 libwayland-cursor0 amd64 1.24.0-2+b1 [12.3 kB] Get: 162 http://deb.debian.org/debian forky/main amd64 libwayland-egl1 amd64 1.24.0-2+b1 [6224 B] Get: 163 http://deb.debian.org/debian forky/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 164 http://deb.debian.org/debian forky/main amd64 libxfixes3 amd64 1:6.0.0-2+b4 [20.2 kB] Get: 165 http://deb.debian.org/debian forky/main amd64 libxcursor1 amd64 1:1.2.3-1 [39.7 kB] Get: 166 http://deb.debian.org/debian forky/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 167 http://deb.debian.org/debian forky/main amd64 libxinerama1 amd64 2:1.1.4-3+b4 [16.0 kB] Get: 168 http://deb.debian.org/debian forky/main amd64 xkb-data all 2.42-1 [790 kB] Get: 169 http://deb.debian.org/debian forky/main amd64 libxkbcommon0 amd64 1.7.0-2.1 [113 kB] Get: 170 http://deb.debian.org/debian forky/main amd64 libxrandr2 amd64 2:1.5.4-1+b3 [36.3 kB] Get: 171 http://deb.debian.org/debian forky/main amd64 libgtk-3-common all 3.24.50-2 [4914 kB] Get: 172 http://deb.debian.org/debian forky/main amd64 libgtk-3-0t64 amd64 3.24.50-2 [2908 kB] Get: 173 http://deb.debian.org/debian forky/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 174 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 175 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 176 http://deb.debian.org/debian forky/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 177 http://deb.debian.org/debian forky/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 178 http://deb.debian.org/debian forky/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 179 http://deb.debian.org/debian forky/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 180 http://deb.debian.org/debian forky/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 181 http://deb.debian.org/debian forky/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 182 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 183 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 184 http://deb.debian.org/debian forky/main amd64 libdrm-intel1 amd64 2.4.125-2 [64.1 kB] Get: 185 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 186 http://deb.debian.org/debian forky/main amd64 libllvm19 amd64 1:19.1.7-3+b2 [26.0 MB] Get: 187 http://deb.debian.org/debian forky/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 188 http://deb.debian.org/debian forky/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 189 http://deb.debian.org/debian forky/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 190 http://deb.debian.org/debian forky/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 191 http://deb.debian.org/debian forky/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 192 http://deb.debian.org/debian forky/main amd64 mesa-libgallium amd64 25.2.2-1 [10.1 MB] Get: 193 http://deb.debian.org/debian forky/main amd64 libgbm1 amd64 25.2.2-1 [45.7 kB] Get: 194 http://deb.debian.org/debian forky/main amd64 libvulkan1 amd64 1.4.321.0-1 [133 kB] Get: 195 http://deb.debian.org/debian forky/main amd64 libgl1-mesa-dri amd64 25.2.2-1 [47.4 kB] Get: 196 http://deb.debian.org/debian forky/main amd64 libglx-mesa0 amd64 25.2.2-1 [116 kB] Get: 197 http://deb.debian.org/debian forky/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 198 http://deb.debian.org/debian forky/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 199 http://deb.debian.org/debian forky/main amd64 libasound2-data all 1.2.14-2 [21.1 kB] Get: 200 http://deb.debian.org/debian forky/main amd64 libasound2t64 amd64 1.2.14-2 [420 kB] Get: 201 http://deb.debian.org/debian forky/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 202 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 203 http://deb.debian.org/debian forky/main amd64 libxtst6 amd64 2:1.2.5-1 [25.8 kB] Get: 204 http://deb.debian.org/debian forky/main amd64 openjdk-21-jre amd64 21.0.9~5ea-1 [219 kB] Get: 205 http://deb.debian.org/debian forky/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 206 http://deb.debian.org/debian forky/main amd64 openjdk-21-jdk-headless amd64 21.0.9~5ea-1 [83.5 MB] Get: 207 http://deb.debian.org/debian forky/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 208 http://deb.debian.org/debian forky/main amd64 openjdk-21-jdk amd64 21.0.9~5ea-1 [3580 kB] Get: 209 http://deb.debian.org/debian forky/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 210 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 211 http://deb.debian.org/debian forky/main amd64 libassuan9 amd64 3.0.2-2 [61.5 kB] Get: 212 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 213 http://deb.debian.org/debian forky/main amd64 gpgconf amd64 2.4.8-3 [129 kB] Get: 214 http://deb.debian.org/debian forky/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 215 http://deb.debian.org/debian forky/main amd64 libnpth0t64 amd64 1.8-3 [23.2 kB] Get: 216 http://deb.debian.org/debian forky/main amd64 gpg amd64 2.4.8-3 [634 kB] Get: 217 http://deb.debian.org/debian forky/main amd64 pinentry-curses amd64 1.3.2-3 [87.8 kB] Get: 218 http://deb.debian.org/debian forky/main amd64 gpg-agent amd64 2.4.8-3 [271 kB] Get: 219 http://deb.debian.org/debian forky/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 220 http://deb.debian.org/debian forky/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 221 http://deb.debian.org/debian forky/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 222 http://deb.debian.org/debian forky/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 223 http://deb.debian.org/debian forky/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 224 http://deb.debian.org/debian forky/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 225 http://deb.debian.org/debian forky/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get: 226 http://deb.debian.org/debian forky/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB] Get: 227 http://deb.debian.org/debian forky/main amd64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get: 228 http://deb.debian.org/debian forky/main amd64 libdevel-callchecker-perl amd64 0.009-2 [15.6 kB] Get: 229 http://deb.debian.org/debian forky/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB] Get: 230 http://deb.debian.org/debian forky/main amd64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get: 231 http://deb.debian.org/debian forky/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 232 http://deb.debian.org/debian forky/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 233 http://deb.debian.org/debian forky/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 234 http://deb.debian.org/debian forky/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 235 http://deb.debian.org/debian forky/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 236 http://deb.debian.org/debian forky/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 237 http://deb.debian.org/debian forky/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 238 http://deb.debian.org/debian forky/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 239 http://deb.debian.org/debian forky/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 240 http://deb.debian.org/debian forky/main amd64 liburi-perl all 5.30-1 [105 kB] Get: 241 http://deb.debian.org/debian forky/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB] Get: 242 http://deb.debian.org/debian forky/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 243 http://deb.debian.org/debian forky/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB] Get: 244 http://deb.debian.org/debian forky/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 245 http://deb.debian.org/debian forky/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 246 http://deb.debian.org/debian forky/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB] Get: 247 http://deb.debian.org/debian forky/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 248 http://deb.debian.org/debian forky/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 249 http://deb.debian.org/debian forky/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 250 http://deb.debian.org/debian forky/main amd64 libnet-ssleay-perl amd64 1.94-3 [339 kB] Get: 251 http://deb.debian.org/debian forky/main amd64 libio-socket-ssl-perl all 2.095-1 [226 kB] Get: 252 http://deb.debian.org/debian forky/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 253 http://deb.debian.org/debian forky/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 254 http://deb.debian.org/debian forky/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 255 http://deb.debian.org/debian forky/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 256 http://deb.debian.org/debian forky/main amd64 libwww-perl all 6.78-1 [183 kB] Get: 257 http://deb.debian.org/debian forky/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 258 http://deb.debian.org/debian forky/main amd64 rsopv amd64 0.6.4-1 [1385 kB] Get: 259 http://deb.debian.org/debian forky/main amd64 wdiff amd64 1.2.2-9 [122 kB] Get: 260 http://deb.debian.org/debian forky/main amd64 devscripts all 2.25.19 [1047 kB] Get: 261 http://deb.debian.org/debian forky/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 262 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 263 http://deb.debian.org/debian forky/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 264 http://deb.debian.org/debian forky/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 265 http://deb.debian.org/debian forky/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 266 http://deb.debian.org/debian forky/main amd64 libnl-3-200 amd64 3.11.0-2 [67.1 kB] Get: 267 http://deb.debian.org/debian forky/main amd64 libnl-route-3-200 amd64 3.11.0-2 [211 kB] Get: 268 http://deb.debian.org/debian forky/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get: 269 http://deb.debian.org/debian forky/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get: 270 http://deb.debian.org/debian forky/main amd64 jarwrapper all 0.81 [9784 B] Get: 271 http://deb.debian.org/debian forky/main amd64 javahelper all 0.81 [79.4 kB] Get: 272 http://deb.debian.org/debian forky/main amd64 libhamcrest-java all 2.2-2 [121 kB] Get: 273 http://deb.debian.org/debian forky/main amd64 junit4 all 4.13.2-5 [350 kB] Get: 274 http://deb.debian.org/debian forky/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 275 http://deb.debian.org/debian forky/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 276 http://deb.debian.org/debian forky/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 277 http://deb.debian.org/debian forky/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 278 http://deb.debian.org/debian forky/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 279 http://deb.debian.org/debian forky/main amd64 junit5 all 5.10.3-1 [2459 kB] Get: 280 http://deb.debian.org/debian forky/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 281 http://deb.debian.org/debian forky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 282 http://deb.debian.org/debian forky/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 283 http://deb.debian.org/debian forky/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 284 http://deb.debian.org/debian forky/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 285 http://deb.debian.org/debian forky/main amd64 libllvm17t64 amd64 1:17.0.6-22+b3 [23.6 MB] Get: 286 http://deb.debian.org/debian forky/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 287 http://deb.debian.org/debian forky/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get: 288 http://deb.debian.org/debian forky/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get: 289 http://deb.debian.org/debian forky/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get: 290 http://deb.debian.org/debian forky/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get: 291 http://deb.debian.org/debian forky/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 292 http://deb.debian.org/debian forky/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 293 http://deb.debian.org/debian forky/main amd64 libasm-java all 9.8-1 [392 kB] Get: 294 http://deb.debian.org/debian forky/main amd64 libatinject-jsr330-api-java all 1.0+ds1-6 [5112 B] Get: 295 http://deb.debian.org/debian forky/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 296 http://deb.debian.org/debian forky/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 297 http://deb.debian.org/debian forky/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 298 http://deb.debian.org/debian forky/main amd64 libcommons-io-java all 2.19.0-1 [524 kB] Get: 299 http://deb.debian.org/debian forky/main amd64 libslf4j-java all 1.7.32-2 [142 kB] Get: 300 http://deb.debian.org/debian forky/main amd64 libmaven-shared-utils-java all 3.4.2-1 [137 kB] Get: 301 http://deb.debian.org/debian forky/main amd64 libcommons-cli-java all 1.6.0-1 [60.4 kB] Get: 302 http://deb.debian.org/debian forky/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 303 http://deb.debian.org/debian forky/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 304 http://deb.debian.org/debian forky/main amd64 libjsr305-java all 0.1~+svn49-12 [26.6 kB] Get: 305 http://deb.debian.org/debian forky/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get: 306 http://deb.debian.org/debian forky/main amd64 libguice-java all 5.1.0-1 [932 kB] Get: 307 http://deb.debian.org/debian forky/main amd64 libmaven-parent-java all 43-2 [6252 B] Get: 308 http://deb.debian.org/debian forky/main amd64 libcommons-lang3-java all 3.17.0-2 [641 kB] Get: 309 http://deb.debian.org/debian forky/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 310 http://deb.debian.org/debian forky/main amd64 libwagon-provider-api-java all 3.5.3-2 [48.3 kB] Get: 311 http://deb.debian.org/debian forky/main amd64 libmaven-resolver-java all 1.9.22-1 [729 kB] Get: 312 http://deb.debian.org/debian forky/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 313 http://deb.debian.org/debian forky/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 314 http://deb.debian.org/debian forky/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 315 http://deb.debian.org/debian forky/main amd64 libplexus-interpolation-java all 1.27-1 [76.8 kB] Get: 316 http://deb.debian.org/debian forky/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 317 http://deb.debian.org/debian forky/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-5 [8444 B] Get: 318 http://deb.debian.org/debian forky/main amd64 libcdi-api-java all 1.2-4 [55.3 kB] Get: 319 http://deb.debian.org/debian forky/main amd64 libsisu-inject-java all 0.3.5-1 [352 kB] Get: 320 http://deb.debian.org/debian forky/main amd64 libsisu-plexus-java all 0.3.5-1 [183 kB] Get: 321 http://deb.debian.org/debian forky/main amd64 libmaven3-core-java all 3.9.9-1 [1661 kB] Get: 322 http://deb.debian.org/debian forky/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 323 http://deb.debian.org/debian forky/main amd64 libmaven-file-management-java all 3.0.0-2 [35.1 kB] Get: 324 http://deb.debian.org/debian forky/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 325 http://deb.debian.org/debian forky/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 326 http://deb.debian.org/debian forky/main amd64 libcatch2-dev amd64 3.7.1-0.6 [646 kB] Get: 327 http://deb.debian.org/debian forky/main amd64 libcommons-collections3-java all 3.2.2-3 [530 kB] Get: 328 http://deb.debian.org/debian forky/main amd64 libcommons-logging-java all 1.3.0-2 [68.6 kB] Get: 329 http://deb.debian.org/debian forky/main amd64 libcommons-beanutils-java all 1.10.1-1.1 [231 kB] Get: 330 http://deb.debian.org/debian forky/main amd64 libcommons-codec-java all 1.18.0-1 [304 kB] Get: 331 http://deb.debian.org/debian forky/main amd64 libcommons-collections4-java all 4.4-2 [682 kB] Get: 332 http://deb.debian.org/debian forky/main amd64 libcommons-compress-java all 1.27.1-2 [641 kB] Get: 333 http://deb.debian.org/debian forky/main amd64 libcommons-digester-java all 1.8.1-7 [138 kB] Get: 334 http://deb.debian.org/debian forky/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 335 http://deb.debian.org/debian forky/main amd64 libcommons-lang-java all 2.6-11 [273 kB] Get: 336 http://deb.debian.org/debian forky/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 337 http://deb.debian.org/debian forky/main amd64 libsnappy1v5 amd64 1.2.2-2 [30.7 kB] Get: 338 http://deb.debian.org/debian forky/main amd64 libsnappy-jni amd64 1.1.10.8-1 [6548 B] Get: 339 http://deb.debian.org/debian forky/main amd64 libsnappy-java all 1.1.10.8-1 [87.8 kB] Get: 340 http://deb.debian.org/debian forky/main amd64 libxz-java all 1.9-1 [143 kB] Get: 341 http://deb.debian.org/debian forky/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 342 http://deb.debian.org/debian forky/main amd64 libmaven-archiver-java all 3.6.2-1 [26.1 kB] Get: 343 http://deb.debian.org/debian forky/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 344 http://deb.debian.org/debian forky/main amd64 libcommons-text-java all 1.13.1-1 [228 kB] Get: 345 http://deb.debian.org/debian forky/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get: 346 http://deb.debian.org/debian forky/main amd64 libcommons-validator-java all 1:1.9.0-1 [191 kB] Get: 347 http://deb.debian.org/debian forky/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 348 http://deb.debian.org/debian forky/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 349 http://deb.debian.org/debian forky/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 350 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 351 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 352 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 353 http://deb.debian.org/debian forky/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 354 http://deb.debian.org/debian forky/main amd64 libnghttp3-dev amd64 1.11.0-1 [101 kB] Get: 355 http://deb.debian.org/debian forky/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 356 http://deb.debian.org/debian forky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 357 http://deb.debian.org/debian forky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 358 http://deb.debian.org/debian forky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 359 http://deb.debian.org/debian forky/main amd64 libunbound8 amd64 1.23.1-1 [606 kB] Get: 360 http://deb.debian.org/debian forky/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 361 http://deb.debian.org/debian forky/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 362 http://deb.debian.org/debian forky/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 363 http://deb.debian.org/debian forky/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 364 http://deb.debian.org/debian forky/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 365 http://deb.debian.org/debian forky/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 366 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 367 http://deb.debian.org/debian forky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 368 http://deb.debian.org/debian forky/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get: 369 http://deb.debian.org/debian forky/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 370 http://deb.debian.org/debian forky/main amd64 libzstd-dev amd64 1.5.7+dfsg-1.1 [389 kB] Get: 371 http://deb.debian.org/debian forky/main amd64 libcurl4-openssl-dev amd64 8.15.0-1 [511 kB] Get: 372 http://deb.debian.org/debian forky/main amd64 libcurlpp0t64 amd64 0.8.1-6 [28.3 kB] Get: 373 http://deb.debian.org/debian forky/main amd64 libcurlpp-dev amd64 0.8.1-6 [59.7 kB] Get: 374 http://deb.debian.org/debian forky/main amd64 libjaxen-java all 1.1.6-5 [214 kB] Get: 375 http://deb.debian.org/debian forky/main amd64 libdom4j-java all 2.1.4-1 [312 kB] Get: 376 http://deb.debian.org/debian forky/main amd64 libdoxia-core-java all 2.0.0-1 [149 kB] Get: 377 http://deb.debian.org/debian forky/main amd64 libplexus-xml-java all 3.0.1-2 [93.7 kB] Get: 378 http://deb.debian.org/debian forky/main amd64 libdoxia-java all 2.0.0-1 [113 kB] Get: 379 http://deb.debian.org/debian forky/main amd64 libmaven-reporting-api-java all 4.0.0-1 [6724 B] Get: 380 http://deb.debian.org/debian forky/main amd64 libxbean-reflect-java all 4.5-9 [132 kB] Get: 381 http://deb.debian.org/debian forky/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 382 http://deb.debian.org/debian forky/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 383 http://deb.debian.org/debian forky/main amd64 velocity all 1.7-7 [431 kB] Get: 384 http://deb.debian.org/debian forky/main amd64 libplexus-velocity-java all 1.2-4 [9676 B] Get: 385 http://deb.debian.org/debian forky/main amd64 liboro-java all 2.0.8a-15 [69.3 kB] Get: 386 http://deb.debian.org/debian forky/main amd64 libvelocity-tools-java all 2.0-9 [311 kB] Get: 387 http://deb.debian.org/debian forky/main amd64 libdoxia-sitetools-java all 2.0.0-1 [176 kB] Get: 388 http://deb.debian.org/debian forky/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 389 http://deb.debian.org/debian forky/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 390 http://deb.debian.org/debian forky/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 391 http://deb.debian.org/debian forky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 392 http://deb.debian.org/debian forky/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 393 http://deb.debian.org/debian forky/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 394 http://deb.debian.org/debian forky/main amd64 libezmorph-java all 1.0.6-4 [75.9 kB] Get: 395 http://deb.debian.org/debian forky/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 396 http://deb.debian.org/debian forky/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get: 397 http://deb.debian.org/debian forky/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get: 398 http://deb.debian.org/debian forky/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 399 http://deb.debian.org/debian forky/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Get: 400 http://deb.debian.org/debian forky/main amd64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get: 401 http://deb.debian.org/debian forky/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get: 402 http://deb.debian.org/debian forky/main amd64 libxml-commons-external-java all 1.4.01-6 [240 kB] Get: 403 http://deb.debian.org/debian forky/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 404 http://deb.debian.org/debian forky/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 405 http://deb.debian.org/debian forky/main amd64 libxom-java all 1.3.9-1 [174 kB] Get: 406 http://deb.debian.org/debian forky/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get: 407 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get: 408 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get: 409 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get: 410 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get: 411 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get: 412 http://deb.debian.org/debian forky/main amd64 libncbi-ngs3 amd64 3.2.1+dfsg-5 [159 kB] Get: 413 http://deb.debian.org/debian forky/main amd64 libngs-jni amd64 3.2.1+dfsg-5 [27.8 kB] Get: 414 http://deb.debian.org/debian forky/main amd64 libngs-java amd64 3.2.1+dfsg-5 [114 kB] Get: 415 http://deb.debian.org/debian forky/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get: 416 http://deb.debian.org/debian forky/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get: 417 http://deb.debian.org/debian forky/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 418 http://deb.debian.org/debian forky/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 419 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get: 420 http://deb.debian.org/debian forky/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get: 421 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-5 [416 kB] Get: 422 http://deb.debian.org/debian forky/main amd64 libltdl-dev amd64 2.5.4-5 [168 kB] Get: 423 http://deb.debian.org/debian forky/main amd64 libhwloc-dev amd64 2.12.2-1 [257 kB] Get: 424 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get: 425 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get: 426 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get: 427 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get: 428 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get: 429 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get: 430 http://deb.debian.org/debian forky/main amd64 libnl-3-dev amd64 3.11.0-2 [110 kB] Get: 431 http://deb.debian.org/debian forky/main amd64 libnl-route-3-dev amd64 3.11.0-2 [235 kB] Get: 432 http://deb.debian.org/debian forky/main amd64 libibverbs-dev amd64 56.1-1 [654 kB] Get: 433 http://deb.debian.org/debian forky/main amd64 libjansi-java all 2.4.1-2 [100 kB] Get: 434 http://deb.debian.org/debian forky/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 435 http://deb.debian.org/debian forky/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 436 http://deb.debian.org/debian forky/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 437 http://deb.debian.org/debian forky/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 438 http://deb.debian.org/debian forky/main amd64 libjetty9-java all 9.4.57-1.1 [2965 kB] Get: 439 http://deb.debian.org/debian forky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 440 http://deb.debian.org/debian forky/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 441 http://deb.debian.org/debian forky/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get: 442 http://deb.debian.org/debian forky/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 443 http://deb.debian.org/debian forky/main amd64 libjtidy-java all 7+svn20110807-6 [251 kB] Get: 444 http://deb.debian.org/debian forky/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 445 http://deb.debian.org/debian forky/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 446 http://deb.debian.org/debian forky/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 447 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-1.1 [357 kB] Get: 448 http://deb.debian.org/debian forky/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 449 http://deb.debian.org/debian forky/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 450 http://deb.debian.org/debian forky/main amd64 libmaven-common-artifact-filters-java all 3.4.0-1 [47.7 kB] Get: 451 http://deb.debian.org/debian forky/main amd64 libmaven-shared-incremental-java all 1.1-6 [9916 B] Get: 452 http://deb.debian.org/debian forky/main amd64 libplexus-compiler-java all 2.13.0-1 [99.5 kB] Get: 453 http://deb.debian.org/debian forky/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 454 http://deb.debian.org/debian forky/main amd64 libplexus-languages-java all 1.1.1-3 [47.8 kB] Get: 455 http://deb.debian.org/debian forky/main amd64 libmaven-compiler-plugin-java all 3.13.0-1 [78.8 kB] Get: 456 http://deb.debian.org/debian forky/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 457 http://deb.debian.org/debian forky/main amd64 libmaven-filtering-java all 3.4.0-1 [51.4 kB] Get: 458 http://deb.debian.org/debian forky/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-5 [11.7 kB] Get: 459 http://deb.debian.org/debian forky/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 460 http://deb.debian.org/debian forky/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 461 http://deb.debian.org/debian forky/main amd64 libmaven-plugin-tools-java all 3.10.2-2 [245 kB] Get: 462 http://deb.debian.org/debian forky/main amd64 libmaven-reporting-exec-java all 2.0.0-1 [23.9 kB] Get: 463 http://deb.debian.org/debian forky/main amd64 libmaven-reporting-impl-java all 4.0.0-1 [17.6 kB] Get: 464 http://deb.debian.org/debian forky/main amd64 libmaven-resources-plugin-java all 3.3.1-1 [27.5 kB] Get: 465 http://deb.debian.org/debian forky/main amd64 libmaven-site-plugin-java all 3.21.0-1 [106 kB] Get: 466 http://deb.debian.org/debian forky/main amd64 libmuparserx4.0.12 amd64 4.0.12-2 [198 kB] Get: 467 http://deb.debian.org/debian forky/main amd64 libmuparserx-dev amd64 4.0.12-2 [38.5 kB] Get: 468 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get: 469 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-9 [3258 kB] Get: 470 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-9 [107 kB] Get: 471 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-9 [203 kB] Get: 472 http://deb.debian.org/debian forky/main amd64 libopenmpi-dev amd64 5.0.8-9 [1228 kB] Get: 473 http://deb.debian.org/debian forky/main amd64 libprotobuf32t64 amd64 3.21.12-11 [983 kB] Get: 474 http://deb.debian.org/debian forky/main amd64 libprotobuf-lite32t64 amd64 3.21.12-11 [274 kB] Get: 475 http://deb.debian.org/debian forky/main amd64 libprotobuf-dev amd64 3.21.12-11 [1328 kB] Get: 476 http://deb.debian.org/debian forky/main amd64 libprotobuf-java all 3.21.12-11 [1267 kB] Get: 477 http://deb.debian.org/debian forky/main amd64 libprotoc32t64 amd64 3.21.12-11 [922 kB] Get: 478 http://deb.debian.org/debian forky/main amd64 libspdlog1.15 amd64 1:1.15.3+ds-1 [109 kB] Get: 479 http://deb.debian.org/debian forky/main amd64 libspdlog-dev amd64 1:1.15.3+ds-1 [91.9 kB] Get: 480 http://deb.debian.org/debian forky/main amd64 libsurefire-java all 2.22.3-4 [1391 kB] Get: 481 http://deb.debian.org/debian forky/main amd64 libwagon-file-java all 3.5.3-2 [8452 B] Get: 482 http://deb.debian.org/debian forky/main amd64 libwagon-http-java all 3.5.3-2 [49.6 kB] Get: 483 http://deb.debian.org/debian forky/main amd64 libxml2-utils amd64 2.14.5+dfsg-0.2 [123 kB] Get: 484 http://deb.debian.org/debian forky/main amd64 maven all 3.9.9-1 [19.7 kB] Get: 485 http://deb.debian.org/debian forky/main amd64 maven-repo-helper all 1.12 [136 kB] Get: 486 http://deb.debian.org/debian forky/main amd64 unzip amd64 6.0-29 [173 kB] Get: 487 http://deb.debian.org/debian forky/main amd64 maven-debian-helper all 2.6.9 [104 kB] Get: 488 http://deb.debian.org/debian forky/main amd64 mpi-default-dev amd64 1.18 [3372 B] Get: 489 http://deb.debian.org/debian forky/main amd64 protobuf-compiler amd64 3.21.12-11 [84.7 kB] Get: 490 http://deb.debian.org/debian forky/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.4 [98.1 kB] Get: 491 http://deb.debian.org/debian forky/main amd64 testng all 6.9.12-4 [795 kB] Get: 492 http://deb.debian.org/debian forky/main amd64 uuid-dev amd64 2.41.1-3 [50.4 kB] Fetched 457 MB in 1min 4s (7086 kB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_258~rc4-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (258~rc4-1) ... Setting up libsystemd-shared:amd64 (258~rc4-1) ... 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 ... 19925 files and directories currently installed.) Preparing to unpack .../systemd_258~rc4-1_amd64.deb ... Unpacking systemd (258~rc4-1) ... Setting up systemd (258~rc4-1) ... 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. Selecting previously unselected package systemd-sysv. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up dbus-session-bus-common (1.16.2-2) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libassuan9:amd64 (3.0.2-2) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up procps (2:4.0.4-9) ... Setting up libxbean-reflect-java (4.5-9) ... Setting up libnl-3-200:amd64 (3.11.0-2) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libplexus-xml-java (3.0.1-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up libopentest4j-java (1.2.0-4) ... Setting up openmpi-common (5.0.8-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up cmake-data (4.1.1+really3.31.6-1) ... Setting up librhash1:amd64 (1.4.6-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libwayland-egl1:amd64 (1.24.0-2+b1) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libprotoc32t64:amd64 (3.21.12-11) ... Setting up libxerces2-java (2.12.2-1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up dbus-system-bus-common (1.16.2-2) ... Creating group 'messagebus' with GID 997. Creating user 'messagebus' (System Message Bus) with UID 997 and GID 997. Setting up libfido2-1:amd64 (1.16.0-2) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up openssl (3.5.2-1) ... Setting up libcatch2-dev (3.7.1-0.6) ... Setting up libdrm-common (2.4.125-2) ... Setting up libcdi-api-java (1.2-4) ... Setting up libsnappy-jni (1.1.10.8-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up liburi-perl (5.30-1) ... Setting up dbus-bin (1.16.2-2) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libfmt10:amd64 (10.1.1+ds1-4) ... Setting up chrpath (0.18-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libxkbcommon0:amd64 (1.7.0-2.1) ... Setting up libwayland-client0:amd64 (1.24.0-2+b1) ... Setting up libnet-ssleay-perl:amd64 (1.94-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libksba8:amd64 (1.6.7-2+b1) ... Setting up pinentry-curses (1.3.2-3) ... Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libwagon-provider-api-java (3.5.3-2) ... Setting up libllvm19:amd64 (1:19.1.7-3+b2) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libjetty9-java (9.4.57-1.1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libplexus-languages-java (1.1.1-3) ... Setting up protobuf-compiler (3.21.12-11) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up jarwrapper (0.81) ... Setting up libtool (2.5.4-5) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libmaven-parent-java (43-2) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-17) ... Setting up libcommons-logging-java (1.3.0-2) ... Setting up libxext6:amd64 (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:amd64 (2.3.8-4) ... Setting up libnss3:amd64 (2:3.114-1) ... Setting up dbus-daemon (1.16.2-2) ... Setting up libxom-java (1.3.9-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-2) ... Setting up libgfortran-15-dev:amd64 (15.2.0-4) ... Setting up libcommons-lang-java (2.6-11) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1) ... Setting up libnl-route-3-200:amd64 (3.11.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up libprotobuf-dev:amd64 (3.21.12-11) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libltdl-dev:amd64 (2.5.4-5) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.5-1) ... Setting up libglib2.0-0t64:amd64 (2.84.4-3) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-22+b3) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b4) ... Setting up testng (6.9.12-4) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up dbus (1.16.2-2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b3) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libfmt-dev:amd64 (10.1.1+ds1-4) ... Setting up libspdlog1.15:amd64 (1:1.15.3+ds-1) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up libcommons-lang3-java (3.17.0-2) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up libnl-3-dev:amd64 (3.11.0-2) ... Setting up groff-base (1.23.0-9) ... Setting up libwayland-cursor0:amd64 (1.24.0-2+b1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ... Setting up gpgconf (2.4.8-3) ... Setting up libpam-systemd:amd64 (258~rc4-1) ... Setting up libcommons-beanutils-java (1.10.1-1.1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libharfbuzz0b:amd64 (11.4.5-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-5) ... Setting up libhwloc-dev:amd64 (2.12.2-1) ... Setting up libsnappy-java (1.1.10.8-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libwagon-file-java (3.5.3-2) ... Setting up libxml2-utils (2.14.5+dfsg-0.2) ... Setting up libcommons-codec-java (1.18.0-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libavahi-client3:amd64 (0.8-17) ... Setting up libio-socket-ssl-perl (2.095-1) ... Setting up gpg (2.4.8-3) ... Created symlink '/etc/systemd/user/sockets.target.wants/keyboxd.socket' -> '/usr/lib/systemd/user/keyboxd.socket'. Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libhttp-message-perl (7.00-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-3) ... Setting up gtk-update-icon-cache (4.20.1+ds-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-7) ... Setting up libibverbs1:amd64 (56.1-1) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up gpg-agent (2.4.8-3) ... 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:amd64 (2.58.0-1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.9~5ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up ibverbs-providers:amd64 (56.1-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up python3.13 (3.13.7-1) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up libcommons-digester-java (1.8.1-7) ... Setting up openssh-client (1:10.0p1-8) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' -> '/usr/lib/systemd/user/ssh-agent.socket'. Setting up libxtst6:amd64 (2:1.2.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libxcursor1:amd64 (1:1.2.3-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b4) ... Setting up libpango-1.0-0:amd64 (1.56.3-2) ... Setting up libdrm-intel1:amd64 (2.4.125-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up libcloudproviders0:amd64 (0.3.6-2) ... Setting up python3 (3.13.7-1) ... Setting up libhwloc-plugins:amd64 (2.12.2-1) ... Setting up libspdlog-dev:amd64 (1:1.15.3+ds-1) ... Setting up man-db (2.13.1-1) ... 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:amd64 (1.18.4-1+b1) ... Setting up libcolord2:amd64 (1.4.8-1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libdconf1:amd64 (0.40.0-5) ... Setting up libnl-route-3-dev:amd64 (3.11.0-2) ... 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:amd64 (3.8.9-3) ... Setting up adwaita-icon-theme (49~rc-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 (0.018-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libatspi2.0-0t64:amd64 (2.58.0-1) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libmaven-common-artifact-filters-java (3.4.0-1) ... Setting up librdmacm1t64:amd64 (56.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libwagon-http-java (3.5.3-2) ... Setting up libcairo-gobject2:amd64 (1.18.4-1+b1) ... Setting up libmaven-shared-utils-java (3.4.2-1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-2) ... Setting up libmaven-resources-plugin-java (3.3.1-1) ... Setting up libcups2t64:amd64 (2.4.10-4) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-3) ... Setting up libncbi-ngs3:amd64 (3.2.1+dfsg-5) ... Setting up libatk-bridge2.0-0t64:amd64 (2.58.0-1) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up mesa-libgallium:amd64 (25.2.2-1) ... Setting up libngs-jni:amd64 (3.2.1+dfsg-5) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.15.0-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcommons-validator-java (1:1.9.0-1) ... Setting up libgbm1:amd64 (25.2.2-1) ... 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:amd64 (0.8.1-6) ... Setting up libgl1-mesa-dri:amd64 (25.2.2-1) ... Setting up debhelper (13.26) ... Setting up dconf-service (0.40.0-5) ... Setting up libibverbs-dev:amd64 (56.1-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up cmake (4.1.1+really3.31.6-1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libngs-java:amd64 (3.2.1+dfsg-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libglx-mesa0:amd64 (25.2.2-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-5) ... Setting up libmaven-archiver-java (3.6.2-1) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libcurl4-openssl-dev:amd64 (8.15.0-1) ... Setting up libcurlpp-dev:amd64 (0.8.1-6) ... Setting up libgtk-3-common (3.24.50-2) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libgtk-3-0t64:amd64 (3.24.50-2) ... Setting up libopenmpi40:amd64 (5.0.8-9) ... Setting up openmpi-bin (5.0.8-9) ... 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:amd64 (5.0.8-9) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-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 (2.25.19) ... Setting up libguava-java (32.0.1-1) ... Setting up javahelper (0.81) ... Setting up libprotobuf-java (3.21.12-11) ... 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 (1.13.1-1) ... 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 (2.41-12) ... Processing triggers for systemd (258~rc4-1) ... 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_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.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: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_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: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: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:amd64 (21.0.9~5ea-1) ... Setting up ant (1.10.15-1) ... Setting up junit4 (4.13.2-5) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.9~5ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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 (1.12) ... 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:amd64 (21.0.9~5ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/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) ... Processing triggers for sgml-base (1.31+nmu1) ... 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 libmaven-reporting-impl-java (4.0.0-1) ... Setting up libsurefire-java (2.22.3-4) ... Setting up maven-debian-helper (2.6.9) ... Processing triggers for ca-certificates (20250419) ... 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: user script /srv/workspace/pbuilder/3078223/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/3078223/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/genomicsdb-1.5.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../genomicsdb_1.5.5-1_source.changes dpkg-buildpackage: info: source package genomicsdb dpkg-buildpackage: info: source version 1.5.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' # 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-1.5.5' dh_autoreconf_clean -O--buildsystem=cmake jh_clean -O--buildsystem=cmake Duplicate specification "unlink|u" 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-1.5.5' # 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=x86_64-linux-gnu cd obj-x86_64-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/x86_64-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=x86_64-linux-gnu .. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.15.0") -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Found LibLZMA: /usr/lib/x86_64-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/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found libuuid: /usr/include -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.5.2") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.15.0") -- 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/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-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 (6.2s) -- Generating done (0.5s) 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-1.5.5/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' # 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=x86_64-linux-gnu cd obj-x86_64-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/x86_64-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=x86_64-linux-gnu .. -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.15.0") 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/x86_64-linux-gnu/libcurl.so (found version "8.15.0") -- 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 (1.3s) -- Generating done (1.8s) -- Build files have been written to: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu # Configuring the Java part using Maven. # First we put the arch triplet in d/maven.properties for the tests. echo "build.triplet=x86_64-linux-gnu" > debian/maven.properties mv pom.xml pom.xml.old sed 's/\${genomicsdb\.version}/1.5.5/; 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-1.5.5/debian/maven-repo make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' 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-1.5.5' dh_auto_build cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/genomicsdb-1.5.5 -B/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/protobuf_ep.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o [ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o [ 8%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o [ 1%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o [ 1%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o [ 1%] Built target protobuf_ep cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/errmod.c [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_gzip.cc [ 1%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle/bitshuffle_core.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/array/array_sorted_read_state.cc [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/kfunc.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/array/array_read_state.cc make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend [ 10%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o [ 10%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/knetfile.c [ 10%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/array/array_sorted_write_state.cc [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o [ 10%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/bcf_sr_sort.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/bgzf.c [ 11%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o [ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o [ 11%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o [ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/array/array.cc [ 10%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/resources /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/array/array_iterator.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 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/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib/kstring.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/c_api/tiledb.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 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-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-1.5.5/genomicsdb-htslib/hfile_net.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_filter.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_filter_bit_shuffle.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/multipart.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_lz4.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_rle.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/codec/codec_zstd.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle/iochain.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/expressions/expression.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/fragment/book_keeping.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/fragment/fragment.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 12%] Generating source/header files from .proto files cd /build/reproducible-path/genomicsdb-1.5.5/src/resources && /usr/bin/protoc --cpp_out=/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources genomicsdb_coordinates.proto genomicsdb_callsets_mapping.proto genomicsdb_export_config.proto genomicsdb_import_config.proto genomicsdb_vid_mapping.proto [ 12%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/fragment/read_state.cc [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/fragment/write_state.cc [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/metadata/metadata.cc /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib/hfile_libcurl.c: In function 'libcurl_open': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib/hfile_libcurl.c:47: /usr/include/x86_64-linux-gnu/curl/curl.h:2923:3: note: declared here 2923 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/regidx.c make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 13%] Built target PROTOBUF_GENERATED_CXX_TARGET [ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o [ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/region.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/error.cc [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/sam.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/metadata/metadata_iterator.cc [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/hilbert_curve.cc [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/mem_utils.cc 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build [ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/progress_bar.cc [ 16%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/query_operations/variant_operations.cc [ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/uri.cc [ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/synced_bcf_reader.c [ 16%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc [ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/misc/utils.cc [ 16%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/query_operations/variant_operations_columnar.cc [ 17%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc [ 17%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/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/storage/storage_buffer.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/storage/storage_buffer.cc [ 19%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/vcf_sweep.c [ 19%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o [ 19%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/tbx.c [ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_fs.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/storage/storage_fs.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant_cell.cc [ 19%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant_field_data.cc [ 20%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant_storage_manager.cc [ 20%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o [ 21%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/textutils.c cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/thread_pool.c [ 21%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant_array_schema.cc [ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant_field_handler.cc [ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/variant.cc [ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/query_variants.cc [ 23%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o [ 23%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc [ 23%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/variant_operations.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/variant_operations_columnar.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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++/15/cstdlib:83, from /usr/include/c++/15/ext/string_conversions.h:45, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api/tiledb.h:44, from /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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__ | ^~~~~~ cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/loader/tiledb_loader_text_file.cc [ 23%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/vcf.c [ 24%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/loader/load_operators.cc [ 24%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/loader/genomicsdb_importer.cc [ 24%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_storage_manager.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:28: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/loader/tiledb_loader_file_base.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_field_data.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_construct.h:61, from /usr/include/c++/15/bits/stl_tempbuf.h:61, from /usr/include/c++/15/memory:68, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_cell.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/gt_remapper.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/gt_remapper_template_definition.h:25, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_array_schema.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_array_schema.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_array_schema.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/query_variants.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/query_variants.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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__ | ^~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/loader/tiledb_loader.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/variant_field_handler.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/storage/storage_manager.cc [ 25%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/vcfutils.c [ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/memory_measure.cc [ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/histogram.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc: In member function 'void BroadCombinedGVCFOperator::handle_INFO_fields(const Variant&)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:622:37: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:643:34: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/cpp/src/query_operations/variant_operations.cc:984:36: note: remove 'std::move' call In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/load_operators.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc: In member function 'void BroadCombinedGVCFOperator::handle_deletions(Variant&)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:1106:37: note: remove 'std::move' call In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/tiledb_loader_text_file.cc:32: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader_file_base.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader_text_file.h:33, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/tiledb_loader_text_file.cc:30: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_codecs.c /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:436:50: note: remove 'std::move' call In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/genomicsdb_importer.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:27: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/vid_mapper_pb.cc [ 27%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_manager_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/storage/storage_manager_config.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/tiledb_loader.cc:27: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/bits/specfun.h:43, from /usr/include/c++/15/cmath:3913, from /usr/include/fmt/format.h:36, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/loader/tiledb_loader.cc:25: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o [ 28%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage/storage_posixfs.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/core/src/storage/storage_posixfs.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_decode.c [ 28%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/storage -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/core/src/codec/external/lz4/lz4.c [ 28%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_encode.c [ 28%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_external.c [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/lut.cc [ 29%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_index.c [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/known_field_info.cc [ 29%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_io.c [ 29%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_samtools.c [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/vid_mapper.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/vid_mapper_sql.cc [ 31%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/cram_stats.c [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/timer.cc [ 32%] 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-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/utils/genomicsdb_logger.cc [ 32%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/mFILE.c [ 32%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/open_trace_file.c [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/vcf/vcf_adapter.cc [ 33%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/pooled_alloc.c [ 33%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/rANS_static.c [ 33%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-htslib/cram/string_alloc.c In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/known_field_info.cc:27: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/gt_common.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/known_field_info.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/known_field_info.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/vcf/vcf2binary.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/config/genomicsdb_config_base.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/vcf/htslib_fs_adapter.cc [ 34%] Building C object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/vcf/hfile_genomicsdb.c [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/config/variant_query_config.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/vid_mapper.cc:33: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/vid_mapper.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/vid_mapper.cc:25: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/config/json_config.cc [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/pb_config.cc.o -MF CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o.d -o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/config/pb_config.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/alleles_combiner.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/alleles_combiner_template_definition.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/annotation_service.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc:23: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/cpp/src/utils/vid_mapper.cc:757:47: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/utils/vid_mapper.cc: In member function 'void FileBasedVidMapper::common_constructor_initialization(const rapidjson::Value&)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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/api/genomicsdb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/genomicsdb.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/genomicsdb_field.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/genomicsdb_plink.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/genomicsdb_utils.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_json_processor.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/cpp/src/api/genomicsdb_json_processor.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/resources/genomicsdb_coordinates.pb.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/config/variant_query_config.cc:26: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/algorithm:62, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/config/variant_query_config.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/vcf/vcf2binary.cc:29: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/vcf/vcf2binary.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/config/genomicsdb_config_base.cc: In member function 'const bool GenomicsDBConfigBase::has_array_name(int) const': /build/reproducible-path/genomicsdb-1.5.5/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)) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/resources/genomicsdb_callsets_mapping.pb.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb_plink.cc:40: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api/genomicsdb.h:37, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api/genomicsdb_plink.h:35, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb_plink.cc:34: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/cpp/src/config/json_config.cc:193:43: note: remove 'std::move' call [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/resources/genomicsdb_export_config.pb.cc [ 39%] Linking C shared library libgenomicsdb-hts.so /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/config/json_config.cc: In member function 'void GenomicsDBImportConfig::read_from_file(const std::string&, int)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/src/main/cpp/src/config/json_config.cc:704:43: note: remove 'std::move' call cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb-hts.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/resources/genomicsdb_import_config.pb.cc [ 40%] Built target genomicsdb-hts [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/resources/genomicsdb_vid_mapping.pb.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb.cc:46: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api/genomicsdb.h:37, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb.cc:34: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 40%] 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 -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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 41%] Linking CXX shared library libgenomicsdb-tiledb.so cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_shared.dir/link.txt --verbose=1 [ 41%] Linking CXX static library libgenomicsdb-tiledb.a cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -P CMakeFiles/tiledb_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_static.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 41%] Built target tiledb_shared /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 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'/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 41%] Built target tiledb_static make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend make -f genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 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/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 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"--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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && 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/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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'/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build [ 41%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/c_api/test_tiledb_utils.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 41%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 41%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/benchmark/test_print_book_keeping.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc [ 41%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/c_api/test_dense_array_api.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build [ 41%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/array/test_array_schema.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 42%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o [ 43%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_posixfs.dir/src/storage_manager/test_posixfs.cc.o -MF CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o.d -o CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/src/storage_manager/test_posixfs.cc [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/codec/test_codec_filter.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/expressions/test_expressions.cc [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/codec/test_codec.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/misc/test_mem_utils.cc [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o [ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o [ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/src/misc/test_uri.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/c_api/test_sparse_array_api.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_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-1.5.5/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc [ 44%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/src/tiledb_array_3d.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/misc/test_uri.cc [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/src/expressions/test_filter_api.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_3d.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/expressions/test_filter_api.cc [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DCATCH2_MAJOR_VERSION=3 -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/catch2 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/array -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/c_api -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/codec -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/expressions -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/fragment -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/metadata -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/misc -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/../core/include/storage -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 46%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_aio_read_dense.cc [ 47%] Linking CXX executable tiledb_array_3d cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_3d.dir/link.txt --verbose=1 [ 48%] Linking CXX executable test_print_array_schema cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_array_schema.dir/link.txt --verbose=1 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake "--color=" [ 48%] Linking CXX executable tiledb_array_aio_read_dense cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_aio_read_dense.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 49%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o [ 49%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_aio_write_dense.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_consolidate.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' In file included from /usr/include/c++/15/bits/basic_string.h:51, from /usr/include/c++/15/string:56: 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++/15/string_view:340:25, inlined from 'std::string_view get_segment(std::string_view, int)' at /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb.cc:819:20: /usr/include/c++/15/string_view:74:5: warning: 'pos' may be used uninitialized [-Wmaybe-uninitialized] 74 | if (__pos > __size) | ^~ /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb.cc: In function 'std::string_view get_segment(std::string_view, int)': /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/src/api/genomicsdb.cc:806:26: note: 'pos' was declared here 806 | std::string::size_type pos; | ^~~ [ 49%] Built target tiledb_array_3d 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 [ 50%] Linking CXX executable tiledb_array_consolidate [ 50%] Linking CXX executable tiledb_array_aio_write_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_aio_write_dense.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_consolidate.dir/link.txt --verbose=1 [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_create_dense.cc [ 50%] Linking CXX executable test_print_book_keeping cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_print_book_keeping.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 50%] Built target tiledb_array_aio_read_dense 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_create_sparse.cc [ 50%] Built target test_print_array_schema 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_iterator_dense.cc 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 50%] Linking CXX executable tiledb_array_create_dense cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_dense.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 51%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse.cc [ 51%] Built target tiledb_array_consolidate 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 51%] Built target tiledb_array_aio_write_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/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 51%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse_filter.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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 [ 51%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_dense.cc [ 52%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_sparse.cc [ 53%] Linking CXX executable tiledb_array_create_sparse cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_create_sparse.dir/link.txt --verbose=1 [ 53%] Linking CXX executable tiledb_array_parallel_consolidate_sparse cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 53%] Built target test_print_book_keeping [ 53%] Linking CXX executable tiledb_array_iterator_dense cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_dense.dir/link.txt --verbose=1 [ 53%] Linking CXX executable tiledb_array_parallel_consolidate_dense cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/link.txt --verbose=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/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 53%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_1.cc 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake "--color=" [ 54%] Linking CXX executable tiledb_array_iterator_sparse cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse.dir/link.txt --verbose=1 [ 54%] Linking CXX executable tiledb_array_iterator_sparse_filter cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_iterator_sparse_filter.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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake "--color=" [ 55%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 55%] 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 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_mpi_io_dense.cc [ 55%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_1.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 55%] Built target tiledb_array_create_dense 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake "--color=" [ 55%] Linking CXX executable tiledb_array_parallel_read_dense_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 [ 55%] Built target tiledb_array_create_sparse make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 56%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_2.cc [ 56%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_1.cc [ 56%] Linking CXX executable tiledb_array_parallel_read_dense_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 56%] Built target tiledb_array_parallel_consolidate_sparse 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 [ 56%] Built target tiledb_array_iterator_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 56%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_2.cc 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake "--color=" [ 57%] Linking CXX executable tiledb_array_parallel_read_mpi_io_dense cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 57%] Linking CXX executable tiledb_array_parallel_read_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/link.txt --verbose=1 [ 57%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_1.cc [ 58%] Linking CXX executable tiledb_array_parallel_write_dense_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 58%] Linking CXX executable tiledb_array_parallel_read_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/link.txt --verbose=1 [ 58%] Built target tiledb_array_iterator_sparse 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 [ 58%] Built target tiledb_array_parallel_consolidate_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend [ 58%] Built target tiledb_array_parallel_read_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake "--color=" [ 58%] Linking CXX executable test_mem_utils cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mem_utils.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 58%] Built target tiledb_array_parallel_read_mpi_io_dense [ 58%] Built target tiledb_array_iterator_sparse_filter 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 59%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_2.cc [ 60%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o [ 59%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o [ 60%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_primitive.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_1.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_3.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 60%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_2.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_mem_utils.dir/link.d CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o -o test_mem_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 60%] Linking CXX executable test_codec_filter cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec_filter.dir/link.txt --verbose=1 [ 60%] Built target test_mem_utils 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 61%] Linking CXX executable tiledb_array_parallel_write_sparse_1 [ 61%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_sorted.cc [ 61%] Linking CXX executable tiledb_array_parallel_write_dense_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.txt --verbose=1 [ 61%] Linking CXX executable tiledb_array_read_dense_3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_3.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 61%] Linking CXX executable tiledb_array_primitive cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_primitive.dir/link.txt --verbose=1 [ 61%] Built target tiledb_array_parallel_read_dense_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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 61%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_1.cc [ 62%] Linking CXX executable tiledb_array_read_dense_1 [ 62%] Linking CXX executable tiledb_array_parallel_write_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_1.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 62%] Built target test_codec_filter 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 [ 63%] Linking CXX executable tiledb_array_read_dense_sorted [ 63%] Linking CXX executable tiledb_array_read_dense_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_2.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_dense_sorted.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 63%] Built target tiledb_array_parallel_read_sparse_1 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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake "--color=" [ 63%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 63%] Built target tiledb_array_parallel_read_sparse_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_1.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 63%] Built target tiledb_array_parallel_write_dense_1 [ 63%] Built target tiledb_array_primitive 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 [ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o 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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_sorted.cc [ 64%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o [ 64%] Built target tiledb_array_parallel_write_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_2.cc 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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 64%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_1.cc [ 64%] Built target tiledb_array_parallel_write_dense_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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 65%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_2.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make 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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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_1.cc 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 [ 66%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o [ 67%] Linking CXX executable tiledb_array_read_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_2.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_2.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake "--color=" [ 67%] Linking CXX executable tiledb_array_read_sparse_1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 67%] Built target tiledb_array_parallel_write_sparse_2 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake "--color=" [ 68%] Linking CXX executable test_codec cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o [ 68%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_2.cc [ 68%] Linking CXX executable tiledb_array_read_sparse_filter_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_1.dir/link.txt --verbose=1 [ 68%] Linking CXX executable tiledb_array_read_sparse_filter_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_filter_2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 68%] Built target tiledb_array_read_dense_1 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake "--color=" [ 68%] Linking CXX executable test_array_schema cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema.dir/link.txt --verbose=1 [ 68%] Linking CXX executable tiledb_array_update_sparse_2 [ 69%] Linking CXX executable tiledb_array_read_sparse_sorted cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_2.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.txt --verbose=1 [ 69%] Linking CXX executable test_uri cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_uri.dir/link.txt --verbose=1 [ 69%] Linking CXX executable tiledb_array_update_dense_2 In file included from /usr/include/string.h:548, from /usr/include/c++/15/cstring:48, 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-1.5.5/genomicsdb-tiledb/test/include/catch2/catch.h:39, from /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:184:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:186:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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; | ^ cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_2.dir/link.txt --verbose=1 In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:191:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:192:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:196:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc:198:11: /usr/include/x86_64-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-1.5.5/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void CATCH2_INTERNAL_TEST_0()': /build/reproducible-path/genomicsdb-1.5.5/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; | ^ make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 69%] Linking CXX executable tiledb_array_update_dense_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_dense_1.dir/link.txt --verbose=1 [ 69%] Linking CXX executable tiledb_array_update_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_update_sparse_1.dir/link.txt --verbose=1 [ 70%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_sorted.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 70%] Linking CXX executable test_filter_api cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_filter_api.dir/link.txt --verbose=1 [ 70%] Built target tiledb_array_read_dense_sorted 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake "--color=" [ 71%] Linking CXX executable tiledb_array_write_dense_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_1.dir/link.txt --verbose=1 [ 71%] Linking CXX executable tiledb_array_write_dense_2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake "--color=" [ 71%] Built target tiledb_array_read_dense_2 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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake "--color=" [ 71%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_1.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_2.cc [ 71%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_3.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 71%] Linking CXX executable tiledb_array_write_dense_sorted cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_dense_sorted.dir/link.txt --verbose=1 [ 71%] Built target test_uri 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 71%] 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_4.cc [ 71%] Built target tiledb_array_read_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 71%] Built target tiledb_array_read_sparse_2 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend [ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_catching_errors.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_clear_delete_move.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 72%] Built target tiledb_array_update_dense_1 [ 72%] Built target tiledb_array_read_sparse_filter_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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend [ 72%] Built target tiledb_array_update_sparse_1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 72%] Built target test_filter_api [ 72%] Built target tiledb_array_read_sparse_filter_2 [ 72%] Built target tiledb_array_update_dense_2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx [ 72%] Built target tiledb_array_read_sparse_sorted [ 72%] Built target test_codec make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/depend [ 72%] Built target test_array_schema make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o [ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o [ 74%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_config.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_ls_workspaces.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_ls.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_iterator.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_delete.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_primitive.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_consolidate.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_create.cc [ 75%] Linking CXX executable tiledb_array_write_sparse_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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/usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake "--color=" [ 75%] Built target tiledb_array_write_dense_2 make -f 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genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 76%] Linking CXX executable tiledb_array_write_sparse_2 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o [ 77%] Linking CXX executable tiledb_clear_delete_move [ 78%] Linking CXX executable tiledb_array_write_sparse_3 [ 78%] Linking CXX executable tiledb_array_write_sparse_4 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_clear_delete_move.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_3.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_write_sparse_4.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_update.cc [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_metadata_write.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 78%] Linking CXX executable tiledb_catching_errors cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_metadata_iterator [ 78%] Built target tiledb_array_write_dense_1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_iterator.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib -I/usr/include/muparserx -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/genomicsdb-tiledb/examples/src/tiledb_workspace_group_create.cc [ 78%] Built target tiledb_array_write_dense_sorted [ 79%] Linking CXX executable tiledb_metadata_read cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_read.dir/link.txt --verbose=1 [ 80%] Linking CXX executable tiledb_metadata_consolidate cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_consolidate.dir/link.txt --verbose=1 [ 81%] Linking CXX executable tiledb_ls [ 79%] Linking CXX executable tiledb_metadata_create [ 79%] Linking CXX executable tiledb_ls_workspaces cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls_workspaces.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_create.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls.dir/link.txt --verbose=1 [ 79%] Linking CXX executable tiledb_config cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_config.dir/link.txt --verbose=1 [ 81%] Linking CXX executable tiledb_metadata_primitive cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_primitive.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 81%] Linking CXX executable tiledb_delete cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_delete.dir/link.txt --verbose=1 [ 81%] Built target tiledb_array_write_sparse_1 [ 81%] Linking CXX executable tiledb_metadata_write cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_write.dir/link.txt --verbose=1 [ 81%] Linking CXX executable tiledb_metadata_update cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Linking CXX executable tiledb_workspace_group_create cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_workspace_group_create.dir/link.txt --verbose=1 [ 82%] Built target tiledb_array_write_sparse_3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_array_write_sparse_2 [ 82%] Built target tiledb_catching_errors /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_metadata_read [ 82%] Built target tiledb_array_write_sparse_4 [ 82%] Built target tiledb_clear_delete_move [ 82%] Built target tiledb_metadata_primitive /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_delete [ 82%] Built target tiledb_metadata_consolidate [ 82%] Built target tiledb_metadata_iterator [ 82%] Built target tiledb_ls [ 82%] Built target tiledb_config [ 82%] Built target tiledb_ls_workspaces /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_metadata_create [ 82%] Built target tiledb_metadata_write /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_update.dir/link.d CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o -o tiledb_metadata_update ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_metadata_update /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 82%] Built target tiledb_workspace_group_create In file included from /usr/include/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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-1.5.5/genomicsdb-tiledb/test/include/catch2/catch.h:39, from /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc:34: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = std::__cxx11::basic_string]', inlined from 'static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = std::__cxx11::basic_string]' at /usr/include/c++/15/bits/alloc_traits.h:649:23, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator >]' at /usr/include/c++/15/bits/stl_vector.h:396:19, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator >]' at /usr/include/c++/15/bits/stl_vector.h:392:7, inlined from 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator >]' at /usr/include/c++/15/bits/stl_vector.h:375:15, inlined from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator >]' at /usr/include/c++/15/bits/stl_vector.h:805:7, inlined from 'std::string readable_size(size_t, bool)' at /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark/tiledb_benchmark.h:496:3: /usr/include/c++/15/bits/new_allocator.h:172:66: warning: 'void operator delete(void*, std::size_t)' called on pointer '__result' with nonzero offset 32 [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc:36: /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark/tiledb_benchmark.h: In function 'std::string readable_size(size_t, bool)': /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test/include/benchmark/tiledb_benchmark.h:483:13: note: declared here 483 | std::string readable_size(size_t size, bool human_readable_sizes) { | ^~~~~~~~~~~~~ [ 83%] Linking CXX executable test_array_iterator cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_iterator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 83%] Linking CXX executable test_storage_buffer cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 test_utils cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_utils.dir/link.txt --verbose=1 [ 83%] Built target test_array_iterator [ 84%] Linking CXX executable test_dense_array_api cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_utils.dir/link.d CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o -o test_utils ../core/libgenomicsdb-tiledb.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 84%] Built target test_storage_buffer [ 84%] Built target test_utils [ 85%] Linking CXX executable test_tiledb_utils cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tiledb_utils.dir/link.txt --verbose=1 [ 85%] Linking CXX executable test_array_schema_api cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema_api.dir/link.txt --verbose=1 [ 86%] Linking CXX executable test_sparse_array_benchmark cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target test_tiledb_utils [ 86%] Built target test_dense_array_api /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target test_array_schema_api /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target test_sparse_array_benchmark [ 86%] Linking CXX executable test_posixfs cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_posixfs.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target GenomicsDB_library_object_files make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Linking CXX static library libgenomicsdb.a [ 86%] Linking CXX shared library libgenomicsdb.so cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledbgenomicsdb.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -P CMakeFiles/genomicsdb.dir/cmake_clean_target.cmake /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fstack-protector-strong -Wall -Wno-reorder 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Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target test_posixfs ct_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/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core: /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 86%] Built target tiledbgenomicsdb make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 86%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o [ 86%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o [ 86%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/jni/src/genomicsdb_jni_init.cc [ 87%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o [ 87%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBQuery.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:29: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api/tiledb.h:44, from /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api/tiledb_utils.h:39, from /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:25: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jlong Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniInitializeGenomicsDBImporterObject(JNIEnv*, jobject, jstring, jint)': /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:102:3: warning: control reaches end of non-void function [-Wreturn-type] 102 | } | ^ /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jlong Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniSetupGenomicsDBLoader(JNIEnv*, jobject, jlong, jstring)': /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:159:3: warning: control reaches end of non-void function [-Wreturn-type] 159 | } | ^ /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc: In function 'jboolean Java_org_genomicsdb_importer_GenomicsDBImporterJni_jniImportBatch(JNIEnv*, jobject, jlong, jlongArray)': /build/reproducible-path/genomicsdb-1.5.5/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:231:3: warning: control reaches end of non-void function [-Wreturn-type] 231 | } | ^ [ 87%] Linking CXX executable test_sparse_array_api cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sparse_array_api.dir/link.txt --verbose=1 [ 87%] Linking CXX executable test_expressions cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 87%] Built target test_sparse_array_api /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libuuid.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so -ldl /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/libCatch2.a -lmuparserx make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 87%] Built target test_expressions [ 87%] Linking CXX shared library libgenomicsdbjni.so cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/src/main:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib libgenomicsdb.so.1.5.4 ../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl ../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 87%] Built target genomicsdbjni _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-1.5.5/obj-x86_64-linux-gnu' [ 87%] Built target genomicsdb make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/depend cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/DependInfo.cmake "--color=" make -f 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'/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -MF CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d -o CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf2genomicsdb.cc make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build make[4]: Leaving directory 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-I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/test_genomicsdb_demo.dir/src/test_genomicsdb_demo.cc.o -MF CMakeFiles/test_genomicsdb_demo.dir/src/test_genomicsdb_demo.cc.o.d -o CMakeFiles/test_genomicsdb_demo.dir/src/test_genomicsdb_demo.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/test_genomicsdb_demo.cc [ 88%] Building CXX object 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-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-1.5.5/src/test/cpp/src/test_multid_vector.cc [ 89%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o [ 89%] Building CXX object tools/CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/ctest_main.cc.o -MF CMakeFiles/ctests.dir/src/ctest_main.cc.o.d -o CMakeFiles/ctests.dir/src/ctest_main.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/ctest_main.cc make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -MF CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o.d -o CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf2genomicsdb_init.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations 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-fopenmp -std=c++17 -fPIE -MD -MT src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o -MF CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d -o CMakeFiles/api_tests.dir/src/ctest_main.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/ctest_main.cc [ 90%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/example/src/test_genomicsdb_bcf_generator.cc [ 90%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o [ 90%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/tools/src/vcf_histogram.cc [ 91%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_config.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_logger.cc [ 91%] Building CXX object tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_htslib_plugin.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o -MF CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d -o CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o -c /build/reproducible-path/genomicsdb-1.5.5/tools/src/create_genomicsdb_workspace.cc [ 91%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o [ 91%] Building CXX object tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/tools/src/consolidate_genomicsdb_array.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_non_diploid_mapper.cc [ 93%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o [ 94%] Building CXX object tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o [ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o [ 93%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o [ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_alleles_combiner.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_gt_remapper.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/tools/src/gt_mpi_gather.cc [ 93%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_query_variants.cc.o [ 95%] Building CXX object example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o [ 93%] Building CXX object tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -I/build/reproducible-path/genomicsdb-1.5.5/tools/include -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/tools/src/vcfdiff.cc [ 93%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o [ 93%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_mem_utils.cc.o cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/example/src/test_genomicsdb_importer.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_pb.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_columnar_gvcf_iterator.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_bgen.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_query_variants.cc cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/genomicsdb-htslib -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb -I/build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core/include/c_api -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/config -I/build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/api -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/include -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/INTERFACE -I/build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/Catch2/single_include -I/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/src/test/cpp/src/test_mem_utils.cc In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/gt_mpi_gather.cc:30: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/gt_mpi_gather.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/reproducible-path/genomicsdb-1.5.5/example/src/test_genomicsdb_bcf_generator.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/example/src/test_genomicsdb_bcf_generator.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/tools/include/vcfdiff.h:31, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcfdiff.cc:25: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/tools/include/vcfdiff.h:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/test_multid_vector.cc:27: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, 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-1.5.5/src/test/cpp/src/test_multid_vector.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/consolidate_genomicsdb_array.cc:29: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/consolidate_genomicsdb_array.cc:26: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf_histogram.cc:24: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf_histogram.cc:23: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/test_non_diploid_mapper.cc:26: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, 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-1.5.5/src/test/cpp/src/test_non_diploid_mapper.cc:24: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/test_query_variants.cc:31: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, 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-1.5.5/src/test/cpp/src/test_query_variants.cc:28: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/src/test_columnar_gvcf_iterator.cc:31: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, 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-1.5.5/src/test/cpp/src/test_columnar_gvcf_iterator.cc:29: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/reproducible-path/genomicsdb-1.5.5/example/src/test_genomicsdb_importer.cc:26: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_iterator_base_funcs.h:68, from /usr/include/c++/15/string:49, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/ios:46, from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/headers.h:32, from /build/reproducible-path/genomicsdb-1.5.5/example/src/test_genomicsdb_importer.cc:25: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/variant_storage_manager.h:30, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/genomicsdb/query_variants.h:28, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/load_operators.h:27, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/loader/tiledb_loader.h:30, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf2genomicsdb.cc:26: /build/reproducible-path/genomicsdb-1.5.5/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++/15/bits/stl_algobase.h:65, from /usr/include/c++/15/bits/hashtable_policy.h:36, from /usr/include/c++/15/bits/hashtable.h:37, from /usr/include/c++/15/bits/unordered_map.h:33, from /usr/include/c++/15/unordered_map:43, from /usr/include/c++/15/functional:65, from /usr/include/spdlog/common.h:13, from /usr/include/spdlog/spdlog.h:12, from /build/reproducible-path/genomicsdb-1.5.5/src/main/cpp/include/utils/genomicsdb_logger.h:41, from /build/reproducible-path/genomicsdb-1.5.5/tools/include/common.h:27, from /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf2genomicsdb.cc:25: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcfdiff.cc: In constructor 'VCFDiffFile::VCFDiffFile(const std::string&, const std::string&)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/tools/src/vcfdiff.cc:83:41: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcfdiff.cc: In member function 'void VCFDiffFile::compare_line(const bcf_hdr_t*, bcf1_t*)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/tools/src/vcfdiff.cc:591:33: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/tools/src/vcfdiff.cc:592:33: note: remove 'std::move' call /build/reproducible-path/genomicsdb-1.5.5/tools/src/vcf2genomicsdb.cc: In function 'int main(int, char**)': /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/tools/src/vcf2genomicsdb.cc:165:45: note: remove 'std::move' call [ 96%] Linking CXX executable test_genomicsdb_bcf_generator cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 96%] Built target test_genomicsdb_bcf_generator [ 96%] Linking CXX executable gt_mpi_gather cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/gt_mpi_gather.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 96%] Built target gt_mpi_gather [ 96%] Linking CXX executable create_genomicsdb_workspace cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 96%] Built target create_genomicsdb_workspace [ 97%] Linking CXX executable vcfdiff [ 97%] Linking CXX executable test_genomicsdb_demo cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdiff.dir/link.txt --verbose=1 cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_demo.dir/link.txt --verbose=1 [ 97%] Linking CXX executable vcf_histogram cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf_histogram.dir/link.txt --verbose=1 [ 98%] Linking CXX executable consolidate_genomicsdb_array cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/consolidate_genomicsdb_array.dir/link.txt --verbose=1 [ 98%] Linking CXX executable test_genomicsdb_importer cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_genomicsdb_importer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 98%] Built target vcfdiff /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 98%] Built target test_genomicsdb_demo [ 98%] Linking CXX executable api_tests cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/api_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 98%] Built target vcf_histogram [ 98%] Built target consolidate_genomicsdb_array /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 98%] Built target test_genomicsdb_importer [ 99%] Linking CXX executable vcf2genomicsdb cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/cmake -E tar xzf /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp/../inputs/test.tgz make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 99%] Built target api_tests /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/genomicsdb-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 99%] Built target vcf2genomicsdb [100%] Linking CXX executable ctests cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib ../../main/libgenomicsdb.a ../../../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../../../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [100%] Built target ctests [100%] Linking CXX executable vcf2genomicsdb_init cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib:/usr/lib/x86_64-linux-gnu/openmpi/lib: ../src/main/libgenomicsdb.a ../genomicsdb-tiledb/core/libgenomicsdb-tiledb.so ../genomicsdb-htslib/libgenomicsdb-hts.so /usr/lib/x86_64-linux-gnu/librt.a /usr/lib/x86_64-linux-gnu/libprotobuf.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl /usr/lib/x86_64-linux-gnu/libfmt.so.10.1.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libmuparserx.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [100%] Built target vcf2genomicsdb_init make[3]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' # 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-1.5.5 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.5/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.5/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 1.5.5 [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-1.5.5/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-1.5.5/build/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.5/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.5/src/main/scala added. [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java:[37,14] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/model/ImportConfig.java:[76,36] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[224,46] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[99,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[109,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[54,27] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[139,58] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[79,39] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[206,31] 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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/build/test [INFO] [copy] Copying 1 file to /build/reproducible-path/genomicsdb-1.5.5/build/test [INFO] [gunzip] Expanding test.tar.gz to /build/reproducible-path/genomicsdb-1.5.5/build/test/test.tar [INFO] [untar] Expanding: /build/reproducible-path/genomicsdb-1.5.5/build/test/test.tar into /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/build/genomicsdb-1.5.5.jar [INFO] [INFO] --- jar:3.3.0:jar (main) @ genomicsdb --- [INFO] Building jar: /build/reproducible-path/genomicsdb-1.5.5/build/genomicsdb-1.5.5-main.jar [INFO] [INFO] --- jar:3.3.0:jar (spark) @ genomicsdb --- [INFO] Building jar: /build/reproducible-path/genomicsdb-1.5.5/build/genomicsdb-1.5.5-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-1.5.5/build [INFO] [move] Moving 1 file to /build/reproducible-path/genomicsdb-1.5.5/build [INFO] Executed tasks [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11.469 s [INFO] Finished at: 2025-09-18T14:36:09+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' dh_auto_test -a || true cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_schema 1: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_print_array_schema 2: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_print_book_keeping 3: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_benchmark 4: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_iterator 5: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_schema_api 6: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_dense_array_api 7: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_api 8: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_tiledb_utils 9: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_codec 10: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_codec_filter 11: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_expressions 12: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 12: Test timeout computed to be: 10000000 test 13 Start 13: test_filter_api 13: Test command: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_filter_api 13: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_mem_utils 14: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_uri 15: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_utils 16: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_posixfs 17: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_storage_buffer 18: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 18: Test timeout computed to be: 10000000 test 19 Start 19: ci_tests 19: Test command: /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples/run_examples.sh "&&" "echo" "Running diff with expected_results" "&&" "diff" "log" "/build/reproducible-path/genomicsdb-1.5.5/examples/expected_results" "&&" "/build/reproducible-path/genomicsdb-1.5.5/examples/run_examples_parallel.sh" 19: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples 19: Test timeout computed to be: 10000000 test 20 Start 20: ctests 20: Test command: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests "-d" "yes" 20: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp 20: Test timeout computed to be: 10000000 test 21 Start 21: api_tests 21: Test command: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/api_tests "-d" "yes" 21: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/tests/test_tools.sh "/build/reproducible-path/genomicsdb-1.5.5/tests/inputs/vcfs" "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools" "1" 22: Working Directory: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools 22: Test timeout computed to be: 10000000 1: Randomness seeded to: 332910677 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-1.5.5/obj-x86_64-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: 2278735304 4: =============================================================================== 4: test cases: 1 | 1 passed 4: assertions: - none - 4: 6: Randomness seeded to: 3718357713 6: =============================================================================== 6: All tests passed (335 assertions in 13 test cases) 6: 9: Randomness seeded to: 3569354000 9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestvk53Td/WORKSPACE.nonexistent does not exist 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestVqBVsL/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTestVqBVsL/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestYjIKyy/WORKSPACE errno=2(No such file or directory) 10: Randomness seeded to: 275405191 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: 11: Randomness seeded to: 976464806 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: 12: Randomness seeded to: 1510947205 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 14: Randomness seeded to: 1023880125 14: Thu Sep 18 14:36:11 2025 Memory stats Tracking memory usage START size=6MB resident=4MB share=3MB text=496KB lib=0 data=536KB dt=0 15: Randomness seeded to: 1514152083 15: =============================================================================== 15: All tests passed (131 assertions in 2 test cases) 15: 16: Randomness seeded to: 525026130 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) 17: Randomness seeded to: 632324567 17: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTest403JRK/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/TileDBTest403JRK/test_posixfs_dirdir errno=21(Is a directory) 17: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTest403JRK/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) 18: Randomness seeded to: 587874792 18: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTesttoJvwq/test-file 18: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTesttoJvwq/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/TileDBTesttoJvwq/test-file 18: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTesttoJvwq/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/TileDBTestLHTYSj/compressed_foo 1/22 Test #1: test_array_schema ................ Passed 0.05 sec 2/22 Test #2: test_print_array_schema .......... Passed 0.05 sec 3/22 Test #3: test_print_book_keeping .......... Passed 0.05 sec 4/22 Test #4: test_sparse_array_benchmark ...... Passed 0.04 sec 5/22 Test #6: test_array_schema_api ............ Passed 0.04 sec 6/22 Test #10: test_codec ....................... Passed 0.03 sec 7/22 Test #11: test_codec_filter ................ Passed 0.03 sec 8/22 Test #15: test_uri ......................... Passed 0.02 sec 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: 19: Example 1: Running ./tiledb_workspace_group_create... 9/22 Test #12: test_expressions ................. Passed 0.03 sec 13: Randomness seeded to: 2997021810 13: =============================================================================== 13: All tests passed (317 assertions in 3 test cases) 13: 10/22 Test #13: test_filter_api .................. Passed 0.05 sec 21: Randomness seeded to: 3772339534 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container/ws 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.911 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-ws 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 21: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-ws errno=2(No such file or directory) 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 21: 14:36:11.911 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container/ws[TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-ws errno=2(No such file or directory) 21: [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported 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 19: Example 3: Running ./tiledb_array_create_dense... 19: Example 3: Done running ./tiledb_array_create_dense 19: Example 4: Running ./tiledb_array_create_sparse... 19: Example 4: Done running ./tiledb_array_create_sparse 19: Example 5: Running ./tiledb_array_primitive... 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... 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) 16: =============================================================================== 16: All tests passed (86 assertions in 6 test cases) 16: 11/22 Test #16: test_utils ....................... Passed 0.42 sec 20: 14:36:12.141 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.141 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.142 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: Randomness seeded to: 879662800 20: 0.125 s: Check loader configuration with json file 20: 14:36:12.143 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.143 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.143 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 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: 14:36:12.144 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.144 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.144 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 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: 14:36:12.145 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.145 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.146 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 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 20: 0.001 s: pb_vid_mapping_test 20: 14:36:12.149 INFO NativeGenomicsDB - pid=3583102 tid=3583102 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: 14:36:12.149 INFO NativeGenomicsDB - pid=3583102 tid=3583102 This is a test 20: 14:36:12.149 WARN NativeGenomicsDB - pid=3583102 tid=3583102 This is a test 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 This is a test 20: 14:36:12.149 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 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: 14:36:12.149 INFO NativeGenomicsDB - pid=3583102 tid=3583102 i=1 str=This is a test 20: 14:36:12.149 WARN NativeGenomicsDB - pid=3583102 tid=3583102 i=2 str=This is a test 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 i=3 str=This is a test 20: 14:36:12.149 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 i=4 str=This is a test 20: 14:36:12.149 INFO NativeGenomicsDB - pid=3583102 tid=3583102 i=6 str=This is a once_only test 20: 14:36:12.149 WARN NativeGenomicsDB - pid=3583102 tid=3583102 i=7 str=This is a once_only test 20: 0.000 s: test logger format 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 i=1 str=This is a test 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Test Exception 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Test Exception 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Test Exception 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Native Stack Trace: 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xb3fb2) [0x55e699a13fb2] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xa4be6) [0x55e699a04be6] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25851c) [0x55e699bb851c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x259018) [0x55e699bb9018] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25947a) [0x55e699bb947a] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c653) [0x55e699b8c653] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c93c) [0x55e699b8c93c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x7a59e) [0x55e6999da59e] 20: /lib/x86_64-linux-gnu/libc.so.6(+0x29ca8) [0x7fb91c033ca8] 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Test Exception 20: 14:36:12.149 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Native Stack Trace: 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xb3fb2) [0x55e699a13fb2] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xa4c09) [0x55e699a04c09] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25851c) [0x55e699bb851c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x259018) [0x55e699bb9018] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25947a) [0x55e699bb947a] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c653) [0x55e699b8c653] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c93c) [0x55e699b8c93c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x7a59e) [0x55e6999da59e] 20: /lib/x86_64-linux-gnu/libc.so.6(+0x29ca8) [0x7fb91c033ca8] 20: 0.000 s: test logger exceptions 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xb3fb2) [0x55e699a13fb2] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xa7d3a) [0x55e699a07d3a] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25851c) [0x55e699bb851c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x259018) [0x55e699bb9018] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25947a) [0x55e699bb947a] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c653) [0x55e699b8c653] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c93c) [0x55e699b8c93c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x7a59e) [0x55e6999da59e] 20: /lib/x86_64-linux-gnu/libc.so.6(+0x29ca8) [0x7fb91c033ca8] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xb3fb2) [0x55e699a13fb2] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xa7d60) [0x55e699a07d60] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25851c) [0x55e699bb851c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x259018) [0x55e699bb9018] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x25947a) [0x55e699bb947a] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c653) [0x55e699b8c653] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x22c93c) [0x55e699b8c93c] 20: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x7a59e) [0x55e6999da59e] 20: /lib/x86_64-linux-gnu/libc.so.6(+0x29ca8) [0x7fb91c033ca8] 20: This is a test 20: 0.000 s: test explicit logger 20: 14:36:12.150 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.150 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.150 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 0.114 s: gvcf iterator 20: 14:36:12.264 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.264 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:12.264 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestDcpjKY/test_file 9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestDcpjKY/test_file 20: 0.025 s: columnar_gvcf_iterator_test 20: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 hts_plugin could not find /tmp/GenomicsDBF4UcpY 20: [TileDB] Error: No TileDB support for URL=dfdfd://ddd. 20: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 htslib_plugin could not open dfdfd://ddd 20: No TileDB support for URL=dfdfd://ddd 20: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 hts_plugin could not find /tmp/GenomicsDBF4UcpY/foo 20: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 hts_plugin could not find /tmp/GenomicsDBF4UcpY/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: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 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: 14:36:12.289 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 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: 0.001 s: test htslib plugin 20: 0.000 s: alleles_combiner 20: 0.000 s: gt_remapper 21: [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 9: =============================================================================== 9: All tests passed (10488239 assertions in 9 test cases) 9: 21: 0.941 s: utils 12/22 Test #9: test_tiledb_utils ................ Passed 0.99 sec 21: 0.000 s: api empty_args 14: Thu Sep 18 14:36:12 2025 Memory stats Tracking memory usage END size=6MB resident=4MB share=4MB text=496KB lib=0 data=536KB dt=0 14: Test rusage 14: user cpu time=0seconds 2546microseconds 14: sys cpu time=0seconds 0microseconds 14: maximum resident set size: 4136KB 14: =============================================================================== 14: test cases: 1 | 1 passed 14: assertions: - none - 14: 13/22 Test #14: test_mem_utils ................... Passed 1.00 sec 21: 0.028 s: api query_variants direct DP 21: 0.011 s: api query_variants direct DP with huge row range 21: 0.011 s: api query_variants direct DP with huge disjoint row ranges 21: 0.017 s: api query_variants direct DP with range composed of multiple points 21: 0.017 s: api query_variants direct DP with range composed of overlapping ranges 21: 14:36:12.789 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 Query interval 0:-100-1 is out of bounds 21: 0.008 s: api query_variants direct DP with invalid row range 21: 0.027 s: api query_variants direct DP and GT 21: 0.019 s: api query_variants direct DP and GT with PP 21: 14:36:12.837 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.837 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.837 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:12.846 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.846 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.847 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:12.856 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.856 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.856 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.021 s: api query_variants with json 21: 14:36:12.857 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.857 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.857 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock 21: 14:36:12.866 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.866 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.866 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:12.875 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:12.875 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:12.875 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.019 s: api query variants with json string 21: 14:36:13.018 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.018 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.018 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.151 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 21: 0.030 s: api query_variant_calls direct 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 17: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestW475H3/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/TileDBTestqReqEJ/test_posixfs_dirread_write/foo 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestqReqEJ/test_posixfs_dirread_write/foo 17: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestqReqEJ/test_posixfs_dirread_write/foo 21: 0.028 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: 0.027 s: api query_variant_calls direct DP and GT with PP 21: 14:36:13.112 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.112 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.112 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 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: 14:36:13.123 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.123 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.124 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.131 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.131 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.131 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.020 s: api query_variant_calls with json 21: 14:36:13.132 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.132 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.132 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.133 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.133 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.133 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.133 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.143 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.143 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.144 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.144 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.144 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.145 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.145 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.156 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.156 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.156 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.157 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.157 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.157 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.157 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with contig intervals instead of tiledb column intervals 21: 0.033 s: api query_variant_calls with protobuf 21: 14:36:13.165 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.165 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.165 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.166 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.166 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.166 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.166 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 18: =============================================================================== 18: All tests passed (450703 assertions in 3 test cases) 18: 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 14/22 Test #18: test_storage_buffer .............. Passed 1.45 sec 21: 14:36:13.177 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.178 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.178 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.178 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.178 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.179 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.179 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.190 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.190 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.190 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.191 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.191 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.191 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.191 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with a filter 21: 0.034 s: api query_variant_calls with protobuf 21: 14:36:13.199 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.199 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.199 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.200 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.200 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.200 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.200 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.212 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.212 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.212 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.213 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.213 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.213 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.213 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.224 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.224 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.225 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.225 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.225 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.226 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.226 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with a filter and workspace with GT ploidy 21: 0.034 s: api query_variant_calls with protobuf 21: 14:36:13.233 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.233 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.234 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.234 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.246 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.246 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.246 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.247 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.247 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.247 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.247 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.258 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.258 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.258 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.259 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.259 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.259 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.259 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with a filter and a small segment size to force TileDB buffers overflow 21: 0.034 s: api query_variant_calls with protobuf 21: 14:36:13.267 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.267 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.267 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.268 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.268 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.268 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.268 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.279 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.279 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.279 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.280 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.280 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.280 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.280 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.291 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.291 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.292 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.292 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.292 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.293 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.293 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with POS and ROW with no match 21: 0.033 s: api query_variant_calls with protobuf 21: 14:36:13.300 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.300 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.301 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.301 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.301 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.302 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.302 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.312 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.312 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.313 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.313 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.313 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.314 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.314 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.324 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.324 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.325 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.325 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.325 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.326 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.326 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with POS and ROW 21: 0.033 s: api query_variant_calls with protobuf 21: 14:36:13.333 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.333 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.334 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.334 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.334 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.335 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.335 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.345 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.345 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.346 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.346 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.346 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.347 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.347 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.357 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.357 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.357 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.358 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.358 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.358 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.358 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with ISHOMREF 21: 0.033 s: api query_variant_calls with protobuf 21: 14:36:13.366 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.366 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.366 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.367 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.367 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.367 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.367 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.377 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.377 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.378 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.378 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.378 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.379 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.379 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.389 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.389 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.390 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.390 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.390 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.391 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.391 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.009 s: Try query with ISHOMREF 21: 0.032 s: api query_variant_calls with protobuf 21: 14:36:13.398 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.398 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.399 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.399 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.410 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.410 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.410 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.411 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.411 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.411 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.411 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.421 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.421 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.422 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.422 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.008 s: Try query with ISHOMREF 21: 0.032 s: api query_variant_calls with protobuf 21: 14:36:13.430 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.430 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.430 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.431 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.431 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.431 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.431 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.441 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.441 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.442 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.442 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.442 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.443 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.443 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.453 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.453 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.453 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.454 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.454 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.454 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.454 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 21: 0.008 s: Try query with ISHOMREF 21: 0.032 s: api query_variant_calls with protobuf 21: 0.006 s: Base configuration 21: 0.007 s: api query_variant_calls with protobuf and config 21: 14:36:13.469 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 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: 0.006 s: Subset Array using QueryConfiguration 21: 0.007 s: api query_variant_calls with protobuf and config 21: 0.006 s: Subset Array using ExportConfiguration 21: 0.007 s: api query_variant_calls with protobuf and config 21: 0.006 s: Subset Array using QueryConfiguration - two intervals 21: 0.007 s: api query_variant_calls with protobuf and config 21: 0.008 s: Subset Array using QueryConfiguration - multiple queries 21: 0.009 s: api query_variant_calls with protobuf and config 21: 0.030 s: Test filter test for 0 21: 0.030 s: api query_variant_calls with protobuf new 21: 0.007 s: Test filter test for 1 21: 0.007 s: api query_variant_calls with protobuf new 21: 0.007 s: Test filter test for 2 21: 0.007 s: api query_variant_calls with protobuf new 21: 0.007 s: Test filter test for 3 21: 0.007 s: api query_variant_calls with protobuf new 21: 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"REF":["C","G"],"GT":["C/C","G/A"],"DP":[null,null]},"HG01530":{"CHR":["1"],"POS":[17385],"REF":["G"],"GT":["G/A"],"DP":[76]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"REF":["C","G"],"GT":["C/C","T/T"],"DP":[null,120]}} 21: 21: 207 {"FIELD":["CHR","POS","REF","GT","DP"],"HG00141":[["1",12141,"C","C/C",null],["1",17385,"G","G/A",null]],"HG01530":[["1",17385,"G","G/A",76]],"HG01958":[["1",12145,"C","C/C",null],["1",17385,"G","T/T",120]]} 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: 1999 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"REF":["C","G"],"QUAL":[null,475.7699890136719],"FILTER":[null,"0"],"DP":[null,null],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DS":["1","1"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MLEAC":[null,"1, 5"],"MLEAF":[null,"0.500000, 1.200000"],"MQ":[null,31.719999313354493],"RAW_MQ":[null,5.5],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"ReadPosRankSum":[null,0.004999999888241291],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"AD":[null,"58, 22, 17"],"DP_FORMAT":[2,80],"GQ":[0,99],"GT":["C/C","G/A"],"MIN_DP":[0,null],"PL":["0, 0, 0","504, 0, 9807, 678, 1870, 2548"],"SB":[null,"58, 0, 22, 0"]},"HG01530":{"CHR":["1"],"POS":[17385],"REF":["G"],"QUAL":[989.77001953125],"FILTER":[null],"DP":[76],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DS":[null],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MLEAC":["1, 0"],"MLEAF":["0.500000, 0.000000"],"MQ":[59.369998931884769],"RAW_MQ":[null],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"ReadPosRankSum":[2.055000066757202],"PGT":[null],"PID":[null],"AD":["40, 36, 0"],"DP_FORMAT":[76],"GQ":[99],"GT":["G/A"],"MIN_DP":[null],"PL":["1018, 0, 1116, 1137, 1224, 2361"],"SB":["9, 31, 13, 23"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"REF":["C","G"],"QUAL":[null,3302.77001953125],"FILTER":[null,"0"],"DP":[null,120],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DS":["1",null],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MLEAC":[null,"2, 7"],"MLEAF":[null,"1.000000, 0.700000"],"MQ":[null,29.81999969482422],"RAW_MQ":[null,2.5],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"ReadPosRankSum":[null,-0.10100000351667404],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"AD":[null,"0, 120, 37"],"DP_FORMAT":[3,120],"GQ":[0,99],"GT":["C/C","T/T"],"MIN_DP":[0,null],"PL":["0, 0, 0","3336, 358, 0, 4536, 958, 7349"],"SB":[null,"0, 0, 0, 0"]}} 21: 21: 0.040 s: api query_variant_calls with JSONVariantCallProcessor 21: 0.000 s: Test genomicsdb demo test case 21: 0.269 s: api generate_vcf direct 21: 14:36:13.860 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.860 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.860 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 0.011 s: api generate_vcf with json 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583494 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583494 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583495 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583495 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583497 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583497 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583498 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583498 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583496 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583496 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583499 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583499 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583494 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583501 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583497 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583498 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583501 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583495 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583502 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583502 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583499 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583496 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.872 DEBUG NativeGenomicsDB - pid=3583106 tid=3583501 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: 14:36:13.872 DEBUG NativeGenomicsDB - pid=3583106 tid=3583502 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 21: api_tests: src/catch2/../catch2/internal/catch_output_redirect.hpp:40: void Catch::OutputRedirect::activate(): Assertion `!m_redirectActive && "redirect is already active"' failed. 21: 21: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 21: api_tests is a Catch2 v3.7.1 host application. 21: Run with -? for options 21: 21: ------------------------------------------------------------------------------- 21: api generate_vcf with json multiple threads 21: ------------------------------------------------------------------------------- 21: ./src/test/cpp/src/test_genomicsdb_api.cc:1314 21: ............................................................................... 21: 21: ./src/test/cpp/src/test_genomicsdb_api.cc:1314: FAILED: 21: {Unknown expression after the reported line} 21: due to a fatal error condition: 21: SIGABRT - Abort (abnormal termination) signal 21: 21: 0.000 s: api generate_vcf with json multiple threads 21: =============================================================================== 21: test cases: 25 | 24 passed | 1 failed 21: assertions: 1493 | 1492 passed | 1 failed 21: 15/22 Test #21: api_tests ........................Subprocess aborted***Exception: 2.16 sec Randomness seeded to: 3772339534 [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.910 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container/ws [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.911 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-ws [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-ws errno=2(No such file or directory) [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 14:36:11.911 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 [TileDB::StorageManagerConfig] Error: HDFS initialization failed for home=az://non-existent-container/ws[TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-ws errno=2(No such file or directory) [TileDB::FileSystem] Error: TileDB built with HDFS support disabled.: Protocol not supported [TileDB::StorageManagerConfig] Error: TileDB built with HDFS support disabled.: Protocol not supported. 0.941 s: utils 0.000 s: api empty_args 0.028 s: api query_variants direct DP 0.011 s: api query_variants direct DP with huge row range 0.011 s: api query_variants direct DP with huge disjoint row ranges 0.017 s: api query_variants direct DP with range composed of multiple points 0.017 s: api query_variants direct DP with range composed of overlapping ranges 14:36:12.789 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 Query interval 0:-100-1 is out of bounds 0.008 s: api query_variants direct DP with invalid row range 0.027 s: api query_variants direct DP and GT 0.019 s: api query_variants direct DP and GT with PP 14:36:12.837 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.837 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.837 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:12.846 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.846 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.847 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:12.856 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.856 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.856 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.021 s: api query_variants with json 14:36:12.857 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.857 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.857 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock 14:36:12.866 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.866 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.866 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:12.875 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:12.875 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:12.875 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.019 s: api query variants with json string 14:36:13.018 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.018 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.018 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.151 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 0.030 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 0.028 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 0.027 s: api query_variant_calls direct DP and GT with PP 14:36:13.112 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.112 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.112 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 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 14:36:13.123 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.123 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.124 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.131 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.131 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.131 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.020 s: api query_variant_calls with json 14:36:13.132 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.132 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.132 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.133 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.133 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.133 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.133 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.143 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.143 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.144 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.144 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.144 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.145 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.145 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.156 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.156 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.156 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.157 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.157 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.157 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.157 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with contig intervals instead of tiledb column intervals 0.033 s: api query_variant_calls with protobuf 14:36:13.165 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.165 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.165 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.166 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.166 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.166 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.166 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.177 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.178 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.178 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.178 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.178 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.179 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.179 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.190 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.190 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.190 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.191 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.191 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.191 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.191 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with a filter 0.034 s: api query_variant_calls with protobuf 14:36:13.199 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.199 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.199 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.200 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.200 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.200 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.200 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.212 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.212 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.212 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.213 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.213 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.213 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.213 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.224 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.224 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.225 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.225 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.225 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.226 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.226 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with a filter and workspace with GT ploidy 0.034 s: api query_variant_calls with protobuf 14:36:13.233 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.233 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.234 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.234 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.234 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.246 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.246 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.246 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.247 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.247 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.247 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.247 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.258 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.258 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.258 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.259 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.259 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.259 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.259 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with a filter and a small segment size to force TileDB buffers overflow 0.034 s: api query_variant_calls with protobuf 14:36:13.267 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.267 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.267 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.268 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.268 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.268 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.268 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.279 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.279 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.279 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.280 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.280 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.280 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.280 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.291 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.291 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.292 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.292 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.292 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.293 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.293 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with POS and ROW with no match 0.033 s: api query_variant_calls with protobuf 14:36:13.300 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.300 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.301 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.301 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.301 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.302 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.302 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.312 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.312 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.313 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.313 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.313 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.314 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.314 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.324 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.324 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.325 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.325 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.325 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.326 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.326 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with POS and ROW 0.033 s: api query_variant_calls with protobuf 14:36:13.333 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.333 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.334 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.334 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.334 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.335 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.335 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.345 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.345 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.346 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.346 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.346 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.347 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.347 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.357 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.357 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.357 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.358 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.358 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.358 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.358 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with ISHOMREF 0.033 s: api query_variant_calls with protobuf 14:36:13.366 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.366 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.366 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.367 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.367 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.367 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.367 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.377 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.377 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.378 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.378 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.378 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.379 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.379 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.389 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.389 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.390 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.390 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.390 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.391 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.391 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.009 s: Try query with ISHOMREF 0.032 s: api query_variant_calls with protobuf 14:36:13.398 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.398 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.399 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.399 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.399 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.410 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.410 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.410 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.411 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.411 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.411 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.411 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.421 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.421 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.422 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.422 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.422 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.008 s: Try query with ISHOMREF 0.032 s: api query_variant_calls with protobuf 14:36:13.430 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.430 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.430 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.431 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.431 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.431 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.431 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.441 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.441 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.442 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.442 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.442 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.443 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.443 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.453 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.453 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.453 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.454 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.454 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize vid mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/vid.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.454 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.454 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize callset mapping file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/callset_t0_1_2.json as protobuf. Trying to parse as a regular JSON file instead 0.008 s: Try query with ISHOMREF 0.032 s: api query_variant_calls with protobuf 0.006 s: Base configuration 0.007 s: api query_variant_calls with protobuf and config 14:36:13.469 ERROR NativeGenomicsDB - pid=3583106 tid=3583106 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 0.006 s: Subset Array using QueryConfiguration 0.007 s: api query_variant_calls with protobuf and config 0.006 s: Subset Array using ExportConfiguration 0.007 s: api query_variant_calls with protobuf and config 0.006 s: Subset Array using QueryConfiguration - two intervals 0.007 s: api query_variant_calls with protobuf and config 0.008 s: Subset Array using QueryConfiguration - multiple queries 0.009 s: api query_variant_calls with protobuf and config 0.030 s: Test filter test for 0 0.030 s: api query_variant_calls with protobuf new 0.007 s: Test filter test for 1 0.007 s: api query_variant_calls with protobuf new 0.007 s: Test filter test for 2 0.007 s: api query_variant_calls with protobuf new 0.007 s: Test filter test for 3 0.007 s: api query_variant_calls with protobuf new 273 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"REF":["C","G"],"GT":["C/C","G/A"],"DP":[null,null]},"HG01530":{"CHR":["1"],"POS":[17385],"REF":["G"],"GT":["G/A"],"DP":[76]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"REF":["C","G"],"GT":["C/C","T/T"],"DP":[null,120]}} 207 {"FIELD":["CHR","POS","REF","GT","DP"],"HG00141":[["1",12141,"C","C/C",null],["1",17385,"G","G/A",null]],"HG01530":[["1",17385,"G","G/A",76]],"HG01958":[["1",12145,"C","C/C",null],["1",17385,"G","T/T",120]]} 37 {"HG00141":2,"HG01530":1,"HG01958":2} 15 {"num_calls":5} 15 {"num_calls":5} 31 ["HG00141","HG01530","HG01958"] 1999 {"HG00141":{"CHR":["1","1"],"POS":[12141,17385],"REF":["C","G"],"QUAL":[null,475.7699890136719],"FILTER":[null,"0"],"DP":[null,null],"BaseQRankSum":[null,-2.0959999561309816],"ClippingRankSum":[null,-1.8589999675750733],"DS":["1","1"],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MLEAC":[null,"1, 5"],"MLEAF":[null,"0.500000, 1.200000"],"MQ":[null,31.719999313354493],"RAW_MQ":[null,5.5],"MQ0":[null,8],"MQRankSum":[null,-0.32899999618530276],"ReadPosRankSum":[null,0.004999999888241291],"PGT":[null,"0|1"],"PID":[null,"17385_G_A"],"AD":[null,"58, 22, 17"],"DP_FORMAT":[2,80],"GQ":[0,99],"GT":["C/C","G/A"],"MIN_DP":[0,null],"PL":["0, 0, 0","504, 0, 9807, 678, 1870, 2548"],"SB":[null,"58, 0, 22, 0"]},"HG01530":{"CHR":["1"],"POS":[17385],"REF":["G"],"QUAL":[989.77001953125],"FILTER":[null],"DP":[76],"BaseQRankSum":[1.0460000038146973],"ClippingRankSum":[-2.242000102996826],"DS":[null],"HaplotypeScore":[null],"InbreedingCoeff":[null],"MLEAC":["1, 0"],"MLEAF":["0.500000, 0.000000"],"MQ":[59.369998931884769],"RAW_MQ":[null],"MQ0":[0],"MQRankSum":[-0.4320000112056732],"ReadPosRankSum":[2.055000066757202],"PGT":[null],"PID":[null],"AD":["40, 36, 0"],"DP_FORMAT":[76],"GQ":[99],"GT":["G/A"],"MIN_DP":[null],"PL":["1018, 0, 1116, 1137, 1224, 2361"],"SB":["9, 31, 13, 23"]},"HG01958":{"CHR":["1","1"],"POS":[12145,17385],"REF":["C","G"],"QUAL":[null,3302.77001953125],"FILTER":[null,"0"],"DP":[null,120],"BaseQRankSum":[null,-2.0739998817443849],"ClippingRankSum":[null,0.5550000071525574],"DS":["1",null],"HaplotypeScore":[null,null],"InbreedingCoeff":[null,null],"MLEAC":[null,"2, 7"],"MLEAF":[null,"1.000000, 0.700000"],"MQ":[null,29.81999969482422],"RAW_MQ":[null,2.5],"MQ0":[null,3],"MQRankSum":[null,-1.36899995803833],"ReadPosRankSum":[null,-0.10100000351667404],"PGT":[null,"0|1"],"PID":[null,"17385_G_T"],"AD":[null,"0, 120, 37"],"DP_FORMAT":[3,120],"GQ":[0,99],"GT":["C/C","T/T"],"MIN_DP":[0,null],"PL":["0, 0, 0","3336, 358, 0, 4536, 958, 7349"],"SB":[null,"0, 0, 0, 0"]}} 0.040 s: api query_variant_calls with JSONVariantCallProcessor 0.000 s: Test genomicsdb demo test case 0.269 s: api generate_vcf direct 14:36:13.860 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.860 WARN NativeGenomicsDB - pid=3583106 tid=3583106 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.860 DEBUG NativeGenomicsDB - pid=3583106 tid=3583106 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 0.011 s: api generate_vcf with json 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583494 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583494 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583495 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583495 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583497 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583497 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583498 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583498 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583496 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583496 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583499 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583499 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583494 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583501 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583497 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583498 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583501 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583495 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583502 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 14:36:13.871 WARN NativeGenomicsDB - pid=3583106 tid=3583502 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583499 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.871 DEBUG NativeGenomicsDB - pid=3583106 tid=3583496 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.872 DEBUG NativeGenomicsDB - pid=3583106 tid=3583501 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 14:36:13.872 DEBUG NativeGenomicsDB - pid=3583106 tid=3583502 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name api_tests: src/catch2/../catch2/internal/catch_output_redirect.hpp:40: void Catch::OutputRedirect::activate(): Assertion `!m_redirectActive && "redirect is already active"' failed. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api_tests is a Catch2 v3.7.1 host application. Run with -? for options ------------------------------------------------------------------------------- api generate_vcf with json multiple threads ------------------------------------------------------------------------------- ./src/test/cpp/src/test_genomicsdb_api.cc:1314 ............................................................................... ./src/test/cpp/src/test_genomicsdb_api.cc:1314: FAILED: {Unknown expression after the reported line} due to a fatal error condition: SIGABRT - Abort (abnormal termination) signal 0.000 s: api generate_vcf with json multiple threads =============================================================================== test cases: 25 | 24 passed | 1 failed assertions: 1493 | 1492 passed | 1 failed 20: 14:36:14.341 INFO NativeGenomicsDB - pid=3583102 tid=3583102 Plink progress 3452039 / 6904084 = 50.00% 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG00141 row: 0 column: 12277 contains a negative value or otherwise did not parse, full string: -2147483648, -2147483648, -2147483648 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG00141 row: 0 column: 12277 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG00141 row: 0 column: 12299 contains a negative value or otherwise did not parse, full string: -2147483648, -2147483648, -2147483648 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG00141 row: 0 column: 12299 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG01958 row: 1 column: 12299 contains a negative value or otherwise did not parse, full string: -2147483648, -2147483648, -2147483648 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG01958 row: 1 column: 12299 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG00141 row: 0 column: 12399 contains a negative value or otherwise did not parse, full string: -2147483648, -2147483648, -2147483648 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG00141 row: 0 column: 12399 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG01958 row: 1 column: 12399 contains a negative value or otherwise did not parse, full string: 0, 1, -2147483648 20: 14:36:14.341 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG01958 row: 1 column: 12399 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan 20: 14:36:14.342 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 GL field for sample: HG00141 row: 0 column: 12499 contains a strictly positive value or otherwise did not parse, full string nan, nan, nan, nan, nan, nan 20: 14:36:14.342 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 PL field for sample: HG01958 row: 1 column: 12499 contains a negative value or otherwise did not parse, full string: -2147483648, -2147483648, -2147483648, -2147483648, -2147483648, -2147483648 20: 14:36:14.342 WARN NativeGenomicsDB - pid=3583102 tid=3583102 GL probabilities at sample: HG01958 row: 1 column: 12499 sum to 0.8981071705534972, expected near 1. Generated BGEN may be invalid 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) 20: 2.318 s: test bgen 20: 14:36:14.609 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 VariantStorageManagerException exception : Could not open workspace 20: 14:36:14.609 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Could not open array non_existent_array in workspace /tmp/GenomicsDBBOOL8U/ws 20: 14:36:14.609 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDBBOOL8U/ws 20: 0.001 s: constructor 20: 14:36:15.018 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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: 14:36:15.018 WARN NativeGenomicsDB - pid=3583102 tid=3583102 Could not deserialize loader file /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead 20: 14:36:15.018 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name 20: 14:36:15.024 ERROR NativeGenomicsDB - pid=3583102 tid=3583102 Invalid query attribute : non_existent_attribute 20: 0.414 s: test basic queries 20: 14:36:15.024 INFO NativeGenomicsDB - pid=3583102 tid=3583102 Mem usage Check basic memory usage rss=49M 20: 0.000 s: check basic memory usage 20: =============================================================================== 20: All tests passed (1439 assertions in 34 test cases) 20: 20: 14:36:15.024 DEBUG NativeGenomicsDB - pid=3583102 tid=3583102 Deleting htslib_fs_adapter tiledb_ctx_map 16/22 Test #20: ctests ........................... Passed 3.30 sec 19: Example 6: Done running ./tiledb_array_write_dense_1 17: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo 19: Example 7: Running ./tiledb_array_write_sparse_1... 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: 17/22 Test #17: test_posixfs ..................... Passed 5.36 sec 19: Example 7: Done running ./tiledb_array_write_sparse_1 5: Randomness seeded to: 370395874 5: [TileDB::Expression] Error: (evaluate_cell) NYI: Filter expressions do not handle empty values yet 5: =============================================================================== 5: All tests passed (527 assertions in 6 test cases) 5: 18/22 Test #5: test_array_iterator .............. Passed 10.94 sec 19: Example 8: Running ./tiledb_ls... 19: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=&& errno=2(No such file or directory) 19: Example 8: Done running ./tiledb_ls 19: Example 9: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 8 i ( 8.1, 8.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 11 llll ( 11.1, 11.2) 19: 12 m ( 12.1, 12.2) 19: 13 nn ( 13.1, 13.2) 19: 14 ooo ( 14.1, 14.2) 19: 15 pppp ( 15.1, 15.2) 19: Example 9: Done running ./tiledb_array_read_dense_1 19: Example 10: Running ./tiledb_array_write_dense_2... 19: Example 10: Done running ./tiledb_array_write_dense_2 7: Randomness seeded to: 3658763175 19: Example 11: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 8 i ( 8.1, 8.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 11 llll ( 11.1, 11.2) 19: 12 m ( 12.1, 12.2) 19: 13 nn ( 13.1, 13.2) 19: 14 ooo ( 14.1, 14.2) 19: 15 pppp ( 15.1, 15.2) 19: Example 11: Done running ./tiledb_array_read_dense_1 19: Example 12: Running ./tiledb_array_read_dense_2... 19: a1 19: ---- 19: Reading cells... 19: 9 19: 11 19: 12 19: Reading cells... 19: 13 19: 14 19: 15 19: Example 12: Done running ./tiledb_array_read_dense_2 19: Example 13: Running ./tiledb_array_write_dense_sorted... 19: Example 13: Done running ./tiledb_array_write_dense_sorted 19: Example 14: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 8 i ( 8.1, 8.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 11 llll ( 11.1, 11.2) 19: 12 m ( 12.1, 12.2) 19: 13 nn ( 13.1, 13.2) 19: 14 ooo ( 14.1, 14.2) 19: 15 pppp ( 15.1, 15.2) 19: Example 14: Done running ./tiledb_array_read_dense_1 19: Example 15: Running ./tiledb_array_update_dense_1... 19: Example 15: Done running ./tiledb_array_update_dense_1 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 (122366175 assertions in 4 test cases) 7: 19/22 Test #7: test_dense_array_api ............. Passed 37.42 sec 19: Example 16: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 8 i ( 8.1, 8.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 11 llll ( 11.1, 11.2) 19: 112 M (112.1, 112.2) 19: 113 NN (113.1, 113.2) 19: 114 OOO (114.1, 114.2) 19: 115 PPPP (115.1, 115.2) 19: Example 16: Done running ./tiledb_array_read_dense_1 19: Example 17: Running ./tiledb_array_update_dense_2... 19: Example 17: Done running ./tiledb_array_update_dense_2 19: Example 18: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 208 u (208.1, 208.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 211 wwww (211.1, 211.2) 19: 212 x (212.1, 212.2) 19: 213 yy (213.1, 213.2) 19: 114 OOO (114.1, 114.2) 19: 115 PPPP (115.1, 115.2) 19: Example 18: Done running ./tiledb_array_read_dense_1 19: Example 19: Running ./tiledb_array_write_sparse_1... 19: Example 19: Done running ./tiledb_array_write_sparse_1 19: Example 20: Running ./tiledb_array_read_sparse_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: (1, 1) 0 a ( 0.1, 0.2) 19: (1, 2) 1 bb ( 1.1, 1.2) 19: (1, 4) 2 ccc ( 2.1, 2.2) 19: (2, 3) 3 dddd ( 3.1, 3.2) 19: (3, 1) 4 e ( 4.1, 4.2) 19: (4, 2) 5 ff ( 5.1, 5.2) 19: (3, 3) 6 ggg ( 6.1, 6.2) 19: (3, 4) 7 hhhh ( 7.1, 7.2) 19: Example 20: Done running ./tiledb_array_read_sparse_1 19: Example 21: Running ./tiledb_array_read_sparse_filter_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: Example 21: Done running ./tiledb_array_read_sparse_filter_1 19: Example 22: Running ./tiledb_array_iterator_sparse... 19: a1 19: ---- 19: 5 19: 6 19: 7 19: Example 22: Done running ./tiledb_array_iterator_sparse 19: Example 23: Running ./tiledb_array_iterator_sparse_filter... 19: a1 19: ---- 19: 6 19: 7 19: Example 23: Done running ./tiledb_array_iterator_sparse_filter 19: Example 24: Running ./tiledb_array_read_sparse_2... 19: a1 19: ---- 19: Reading cells... 19: 5 19: 6 19: Reading cells... 19: 7 19: Example 24: Done running ./tiledb_array_read_sparse_2 19: Example 25: Running ./tiledb_array_read_sparse_filter_2... 19: a1 19: ---- 19: Reading cells... 19: 6 19: Reading cells... 19: 7 19: Example 25: Done running ./tiledb_array_read_sparse_filter_2 19: Example 26: Running ./tiledb_array_write_sparse_2... 8: Randomness seeded to: 3694631899 19: Example 26: Done running ./tiledb_array_write_sparse_2 8: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== 8: All tests passed (13207510 assertions in 15 test cases) 8: 20/22 Test #8: test_sparse_array_api ............ Passed 57.15 sec 19: Example 27: Running ./tiledb_array_read_sparse_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: (1, 1) 0 a ( 0.1, 0.2) 19: (1, 2) 1 bb ( 1.1, 1.2) 19: (1, 4) 2 ccc ( 2.1, 2.2) 19: (2, 3) 3 dddd ( 3.1, 3.2) 19: (3, 1) 4 e ( 4.1, 4.2) 19: (4, 2) 5 ff ( 5.1, 5.2) 19: (3, 3) 6 ggg ( 6.1, 6.2) 19: (3, 4) 7 hhhh ( 7.1, 7.2) 19: Example 27: Done running ./tiledb_array_read_sparse_1 19: Example 28: Running ./tiledb_array_read_sparse_2... 19: a1 19: ---- 19: Reading cells... 19: 5 19: 6 19: Reading cells... 19: 7 19: Example 28: Done running ./tiledb_array_read_sparse_2 19: Example 29: Running ./tiledb_array_read_sparse_filter_2... 19: a1 19: ---- 19: Reading cells... 19: 6 19: Reading cells... 19: 7 19: Example 29: Done running ./tiledb_array_read_sparse_filter_2 19: Example 30: Running ./tiledb_array_update_sparse_1... 19: Example 30: Done running ./tiledb_array_update_sparse_1 22: Build with DISABLE_MPI option set, not running gt_mpi_gather tests 21/22 Test #22: tools_tests ...................... Passed 65.94 sec 19: Example 31: Running ./tiledb_array_read_sparse_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: (1, 1) 0 a ( 0.1, 0.2) 19: (1, 2) 1 bb ( 1.1, 1.2) 19: (1, 4) 2 ccc ( 2.1, 2.2) 19: (2, 3) 3 dddd ( 3.1, 3.2) 19: (3, 1) 4 e ( 4.1, 4.2) 19: (3, 2) 104 u (104.1, 104.2) 19: (4, 1) 105 vvvv (105.1, 105.2) 19: (4, 2) 5 ff ( 5.1, 5.2) 19: (3, 3) 106 w (106.1, 106.2) 19: (3, 4) 107 yyy (107.1, 107.2) 19: Example 31: Done running ./tiledb_array_read_sparse_1 19: Example 32: Running ./tiledb_array_read_sparse_filter_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: (4, 1) 105 vvvv (105.1, 105.2) 19: Example 32: Done running ./tiledb_array_read_sparse_filter_1 19: Example 33: Running ./tiledb_array_read_sparse_filter_2... 19: a1 19: ---- 19: Reading cells... 19: Reading cells... 19: 106 19: 107 19: Example 33: Done running ./tiledb_array_read_sparse_filter_2 19: Example 34: Running ./tiledb_array_iterator_sparse... 19: a1 19: ---- 19: 104 19: 5 19: 106 19: 107 19: Example 34: Done running ./tiledb_array_iterator_sparse 19: Example 35: Running ./tiledb_array_iterator_sparse_filter... 19: a1 19: ---- 19: 104 19: 106 19: 107 19: Example 35: Done running ./tiledb_array_iterator_sparse_filter 19: Example 36: Running ./tiledb_array_read_sparse_2... 19: a1 19: ---- 19: Reading cells... 19: 104 19: 5 19: Reading cells... 19: 106 19: 107 19: Example 36: Done running ./tiledb_array_read_sparse_2 19: Example 37: Running ./tiledb_array_consolidate... 19: Example 37: Done running ./tiledb_array_consolidate 19: Example 38: Running ./tiledb_array_read_dense_1... 19: a1 a2 (a3.first, a3.second) 19: ----------------------------------------- 19: 0 a ( 0.1, 0.2) 19: 1 bb ( 1.1, 1.2) 19: 2 ccc ( 2.1, 2.2) 19: 3 dddd ( 3.1, 3.2) 19: 4 e ( 4.1, 4.2) 19: 5 ff ( 5.1, 5.2) 19: 6 ggg ( 6.1, 6.2) 19: 7 hhhh ( 7.1, 7.2) 19: 208 u (208.1, 208.2) 19: 9 jj ( 9.1, 9.2) 19: 10 kkk ( 10.1, 10.2) 19: 211 wwww (211.1, 211.2) 19: 212 x (212.1, 212.2) 19: 213 yy (213.1, 213.2) 19: 114 OOO (114.1, 114.2) 19: 115 PPPP (115.1, 115.2) 19: Example 38: Done running ./tiledb_array_read_dense_1 19: Example 39: Running ./tiledb_array_read_sparse_1... 19: coords a1 a2 (a3.first, a3.second) 19: -------------------------------------------------- 19: (1, 1) 0 a ( 0.1, 0.2) 19: (1, 2) 1 bb ( 1.1, 1.2) 19: (1, 4) 2 ccc ( 2.1, 2.2) 19: (2, 3) 3 dddd ( 3.1, 3.2) 19: (3, 1) 4 e ( 4.1, 4.2) 19: (3, 2) 104 u (104.1, 104.2) 19: (4, 1) 105 vvvv (105.1, 105.2) 19: (4, 2) 5 ff ( 5.1, 5.2) 19: (3, 3) 106 w (106.1, 106.2) 19: (3, 4) 107 yyy (107.1, 107.2) 19: Example 39: Done running ./tiledb_array_read_sparse_1 19: Example 40: Running ./tiledb_array_read_dense_2... 19: a1 19: ---- 19: Reading cells... 19: 9 19: 211 19: 212 19: Reading cells... 19: 213 19: 114 19: 115 19: Example 40: Done running ./tiledb_array_read_dense_2 19: Example 41: Running ./tiledb_array_read_sparse_2... 19: a1 19: ---- 19: Reading cells... 19: 104 19: 5 19: Reading cells... 19: 106 19: 107 19: Example 41: Done running ./tiledb_array_read_sparse_2 19: Example 42: Running ./tiledb_array_3d... 19: 4 results 19: coords a1 a2 19: ----------------------- 19: 0, 0, 0 0 first 19: 0, 0, 1 1 second 19: 0, 2, 3 2 third 19: 2, 1, 1 3 fourth 19: Example 42: Done running ./tiledb_array_3d 22/22 Test #19: ci_tests ......................... Passed 80.83 sec 95% tests passed, 1 tests failed out of 22 Total Test time (real) = 81.00 sec The following tests FAILED: 21 - api_tests (Subprocess aborted) Errors while running CTest make[2]: *** [Makefile:74: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 returned exit code 2 make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' dh_auto_build cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/genomicsdb-1.5.5 -B/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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/bitshuffle/iochain.c.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_blosc.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_filter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_filter_bit_shuffle.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_filter_delta_encode.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_gzip.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_lz4.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_rle.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/codec/codec_zstd.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target genomicsdb-hts 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/fragment/read_state.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build.make genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/resources /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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/uri.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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_fs.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target TILEDB_CORE_OBJECTS [ 13%] Built target genomicsdb-hts make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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_vid_mapping.pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_field.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_json_processor.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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/genomicsdb/genomicsdb_columnar_field.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/genomicsdb_iterators.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/genomicsdb_multid_vector_field.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/query_variants.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/variant.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/variant_array_schema.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/cpp/src/genomicsdb/variant_cell.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/variant_field_data.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb/variant_field_handler.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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/genomicsdb/variant_storage_manager.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/genomicsdb_importer.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/load_operators.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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/query_operations/broad_combined_gvcf.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/query_operations/broad_combined_gvcf_columnar.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/query_operations/variant_operations.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/query_operations/variant_operations_columnar.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/alleles_combiner_gvcf_columnar_iterator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake "--color=" Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/histogram.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/known_field_info.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/lut.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/memory_measure.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/timer.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/vid_mapper.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/vid_mapper_pb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/utils/vid_mapper_sql.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/vcf/genomicsdb_bcf_generator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/vcf/htslib_fs_adapter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/vcf/vcf2binary.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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/vcf/vcf_adapter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build Dependencies file "genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_shared make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 25%] Built target tiledb_static Consolidate compiler generated dependencies of target GenomicsDB_library_object_files [ 26%] Built target tiledb_shared make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/depend Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_sparse_array_benchmark make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". 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 Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". 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 Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_print_array_schema Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_dense_array_api Consolidate compiler generated dependencies of target test_array_iterator Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.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 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_tiledb_utils Consolidate compiler generated dependencies of target test_codec_filter make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_sparse_array_api Consolidate compiler generated dependencies of target test_mem_utils make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". 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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_codec Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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 Consolidate compiler generated dependencies of target test_uri 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_3d 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build [ 38%] Built target test_array_schema [ 41%] 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/build Consolidate compiler generated dependencies of target test_storage_buffer make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_utils Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_3d.dir/build Consolidate compiler generated dependencies of target tiledb_array_aio_read_dense make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build Consolidate compiler generated dependencies of target test_posixfs make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/src/tiledb_array_aio_write_dense.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". 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 -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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build'. make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_aio_write_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_filter_api 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_filter_api.dir/build Consolidate compiler generated dependencies of target tiledb_array_consolidate make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build [ 42%] Built target test_dense_array_api make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 42%] Built target test_expressions [ 43%] Built target test_print_array_schema [ 44%] Built target test_sparse_array_benchmark [ 45%] Built target test_array_iterator [ 46%] Built target test_array_schema_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend [ 46%] Built target test_print_book_keeping 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/depend [ 47%] Built target test_sparse_array_api make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake "--color=" [ 48%] Built target test_mem_utils [ 49%] Built target test_codec 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake "--color=" [ 49%] Built target test_tiledb_utils 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake "--color=" [ 49%] Built target test_uri [ 50%] Built target test_filter_api [ 50%] Built target test_codec_filter make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake "--color=" [ 50%] Built target tiledb_array_aio_read_dense [ 51%] Built target test_posixfs 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 [ 52%] Built target test_utils make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake "--color=" [ 54%] Built target tiledb_array_aio_write_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend [ 54%] Built target tiledb_array_consolidate make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake "--color=" [ 54%] Built target test_storage_buffer make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend 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 [ 55%] Built target tiledb_array_3d make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake "--color=" 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 -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 -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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend 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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_array_create_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_array_create_sparse 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_dense make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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_iterator_dense.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_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-1.5.5/obj-x86_64-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_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.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-1.5.5/obj-x86_64-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_2.dir/src/tiledb_array_parallel_read_dense_2.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_mpi_io_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_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/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_iterator_dense Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse_filter Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 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of target tiledb_array_parallel_consolidate_sparse Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_2 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_filter.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.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/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-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_write_dense_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-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_read_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_1 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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". 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 -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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_2 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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_3.dir/src/tiledb_array_read_dense_3.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_primitive Consolidate compiler generated dependencies of target tiledb_array_read_dense_3 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_dense_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_dense_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_dense_sorted [ 56%] Built target tiledb_array_create_sparse 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 56%] Built target tiledb_array_create_dense [ 57%] Built target tiledb_array_iterator_sparse_filter [ 57%] Built target tiledb_array_iterator_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 58%] Built target tiledb_array_parallel_consolidate_dense [ 58%] Built target tiledb_array_parallel_consolidate_sparse [ 59%] Built target tiledb_array_parallel_read_mpi_io_dense make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' [ 60%] Built target tiledb_array_parallel_read_dense_1 [ 61%] Built target tiledb_array_iterator_sparse [ 60%] Built target tiledb_array_parallel_read_dense_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 [ 62%] Built target tiledb_array_parallel_write_sparse_1 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 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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 [ 63%] Built target tiledb_array_parallel_read_sparse_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.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 [ 63%] Built target tiledb_array_parallel_read_sparse_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake "--color=" [ 64%] Built target tiledb_array_parallel_write_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.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/depend [ 63%] Built target tiledb_array_parallel_write_sparse_2 [ 65%] Built target tiledb_array_read_dense_sorted [ 65%] Built target tiledb_array_parallel_write_dense_2 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake "--color=" [ 66%] Built target tiledb_array_read_dense_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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake "--color=" 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 [ 67%] Built target tiledb_array_primitive make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake "--color=" 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 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/compiler_depend.internal". [ 68%] Built target tiledb_array_read_dense_3 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/depend make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.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 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend 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-1.5.5/obj-x86_64-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_1.dir/src/tiledb_array_read_sparse_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake "--color=" [ 68%] Built target tiledb_array_read_dense_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake "--color=" 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_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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_1.dir/src/tiledb_array_write_dense_1.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake "--color=" make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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_4.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake "--color=" 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake "--color=" Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.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-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/tiledbgenomicsdb.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdb.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 68%] 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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/DependInfo.cmake "--color=" 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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/DependInfo.cmake "--color=" make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend 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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.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-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_array_write_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_sorted Consolidate compiler generated dependencies of target tiledb_array_write_dense_1 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_1 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_2 Consolidate compiler generated dependencies of target tiledb_array_write_sparse_4 Consolidate compiler generated dependencies of target tiledb_metadata_consolidate Consolidate compiler generated dependencies of target tiledb_array_update_dense_1 Consolidate compiler generated dependencies of target tiledb_ls Consolidate compiler generated dependencies of target tiledb_array_write_sparse_3 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_catching_errors Consolidate compiler generated dependencies of target tiledb_metadata_read Consolidate compiler generated dependencies of target tiledb_workspace_group_create make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_update make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 Consolidate compiler generated dependencies of target tiledb_array_update_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_write_dense_2 Consolidate compiler generated dependencies of target tiledb_clear_delete_move make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledbgenomicsdb make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target tiledb_ls_workspaces make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_config Consolidate compiler generated dependencies of target tiledb_array_write_dense_sorted make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_create make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_write_sparse_1 Consolidate compiler generated dependencies of target tiledb_array_update_dense_2 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_delete make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_update_sparse_1 make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_iterator make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_write make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_primitive make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/build'. 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". 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 Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target consolidate_genomicsdb_array Consolidate compiler generated dependencies of target test_genomicsdb_demo Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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 Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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 Dependencies file "tools/CMakeFiles/vcf2genomicsdb_init.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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 "src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcfdiff.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_mem_utils.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". 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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/gt_mpi_gather.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/compiler_depend.internal". 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 -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_query_variants.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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 -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.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 make[4]: Nothing to be done for 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'/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' 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[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make -f src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build.make src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/tiledbgenomicsdb.dir/build'. make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/consolidate_genomicsdb_array.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target api_tests make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/test_genomicsdb_demo.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target vcf2genomicsdb_init Consolidate compiler generated dependencies of target vcfdiff Consolidate compiler generated dependencies of target vcf2genomicsdb Consolidate compiler generated dependencies of target create_genomicsdb_workspace make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target ctests make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target gt_mpi_gather make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/create_genomicsdb_workspace.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build [ 69%] Built target tiledb_array_read_sparse_filter_2 make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/build [ 69%] Built target tiledb_array_read_sparse_filter_1 make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 69%] Built target tiledb_array_read_sparse_1 [ 69%] Built target tiledb_array_update_sparse_1 [ 70%] Built target tiledb_array_read_sparse_2 make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build [ 71%] Built target tiledb_array_write_dense_1 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb_init.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 72%] Built target tiledb_array_update_sparse_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_read_sparse_sorted make[4]: Nothing to be done for 'tools/CMakeFiles/gt_mpi_gather.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_write_dense_2 make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcfdiff.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_update_dense_1 make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/api_tests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/ctests.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 74%] Built target tiledb_array_update_dense_2 [ 75%] Built target tiledb_array_write_dense_sorted [ 76%] Built target tiledb_array_write_sparse_3 [ 77%] Built target tiledb_clear_delete_move [ 77%] Built target tiledb_array_write_sparse_2 [ 78%] Built target tiledb_array_write_sparse_1 [ 78%] Built target tiledb_array_write_sparse_4 [ 78%] Built target tiledb_config [ 79%] Built target tiledb_metadata_consolidate [ 80%] Built target tiledb_metadata_iterator [ 81%] Built target tiledb_catching_errors [ 82%] Built target tiledb_delete [ 83%] Built target tiledb_ls [ 83%] Built target tiledb_ls_workspaces [ 83%] Built target tiledb_metadata_create make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend [ 83%] Built target tiledb_metadata_write make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend [ 84%] Built target tiledb_metadata_update [ 85%] Built target consolidate_genomicsdb_array [ 85%] Built target test_genomicsdb_demo [ 86%] Built target tiledb_metadata_primitive [ 86%] Built target tiledb_metadata_read make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/example /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake "--color=" make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend [ 87%] Built target tiledb_workspace_group_create [ 87%] Built target tiledbgenomicsdb make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/example /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake "--color=" [ 88%] Built target gt_mpi_gather make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend [ 89%] Built target vcf2genomicsdb [ 89%] Built target vcf2genomicsdb_init make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 89%] Built target create_genomicsdb_workspace cd /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/genomicsdb-1.5.5 /build/reproducible-path/genomicsdb-1.5.5/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake "--color=" [ 94%] Built target ctests [ 96%] Built target api_tests [ 95%] Built target vcfdiff Dependencies file "example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/compiler_depend.internal". Dependencies file "example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/compiler_depend.internal". Dependencies file "example/CMakeFiles/test_genomicsdb_bcf_generator.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/compiler_depend.internal". Dependencies file "example/CMakeFiles/test_genomicsdb_importer.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "tools/CMakeFiles/vcf_histogram.dir/link.d" is newer than depends file "/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target vcf_histogram 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-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build 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 Consolidate compiler generated dependencies of target genomicsdbjni make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-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-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_importer.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf_histogram.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdbjni.dir/build'. make[4]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' [ 97%] Built target test_genomicsdb_importer [ 99%] Built target vcf_histogram [ 99%] Built target test_genomicsdb_bcf_generator [100%] Built target genomicsdbjni make[3]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' # Testing the Java part. We extend LD_LIBRARY_PATH because some test code is # run without surefire. LD_LIBRARY_PATH=":obj-x86_64-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-1.5.5 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.5/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.5/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 1.5.5 [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-1.5.5/build/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.5/src/main/java added. [INFO] Source directory: /build/reproducible-path/genomicsdb-1.5.5/src/main/scala added. [INFO] [INFO] --- resources:3.3.1:resources (default-resources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java:[37,14] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/model/ImportConfig.java:[76,36] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[224,46] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[99,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[109,19] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[395,80] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[54,27] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/model/CommandLineImportConfig.java:[139,58] previous possible 'this' escape happens here via invocation [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[79,39] possible 'this' escape before subclass is fully initialized [WARNING] /build/reproducible-path/genomicsdb-1.5.5/src/main/java/org/genomicsdb/reader/GenomicsDBFeatureReader.java:[206,31] 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-1.5.5/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-1.5.5/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-1.5.5/src/test/resources [INFO] [INFO] --- antrun:3.1.0:run (unzip-test-artifacts) @ genomicsdb --- [INFO] Executing tasks [INFO] [untar] Expanding: /build/reproducible-path/genomicsdb-1.5.5/build/test/test.tar into /build/reproducible-path/genomicsdb-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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-1.5.5/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 ERROR StatusLogger Reconfiguration failed: No configuration found for '639fee48' at 'null' in 'null' 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 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.01648196,Cpu time(s),0.0065689500000000005 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.002323812,Cpu time(s),0.002353194 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.004592348,Cpu time(s),9.882839999999999E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.5023E-4,Cpu time(s),6.33865E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),9.92948E-4,Cpu time(s),8.98179E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),5.37586E-4,Cpu time(s),4.06925E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),5.67224E-4,Cpu time(s),4.00572E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),8.42623E-4,Cpu time(s),7.03345E-4 [INFO] Tests run: 46, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.318 s - in TestSuite [INFO] [INFO] Results: [INFO] [INFO] Tests run: 46, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:09 min [INFO] Finished at: 2025-09-18T14:38:48+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' # Installing the Java part. dh_auto_install --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-1.5.5 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.5/debian -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.5/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/genomicsdb-1.5.5/debian -Ddebian.package=libgenomicsdb-java -Dmaven.repo.local=/build/reproducible-path/genomicsdb-1.5.5/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install 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 1.5.5 [INFO] from pom.xml [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian:2.6:install (default-cli) @ genomicsdb --- [INFO] Cleaning pom file: /build/reproducible-path/genomicsdb-1.5.5/pom.xml.save with options: [INFO] --keep-pom-version --package=libgenomicsdb-java [INFO] --rules=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.rules [INFO] --ignore-rules=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.ignoreRules [INFO] --published-rules=/build/reproducible-path/genomicsdb-1.5.5/debian/maven.publishedRules [INFO] Install jar for genomicsdb into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.354 s [INFO] Finished at: 2025-09-18T14:38:54+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibgenomicsdb-java --base-directory=/build/reproducible-path/genomicsdb-1.5.5 --non-explore Analysing pom.xml... mh_unpatchpoms -plibgenomicsdb-java make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' dh_auto_install -O--buildsystem=cmake -Nlibgenomicsdb-java cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/genomicsdb-1.5.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/genomicsdb-1.5.5 -B/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/faidx.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/kbitset.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hts.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/tbx.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/regidx.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hfile.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/knetfile.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/cram.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hts_log.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/vcf_sweep.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/vcfutils.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/kfunc.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/kroundup.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/vcf.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/sam.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/synced_bcf_reader.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/kstring.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hts_os.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/khash_str2int.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hts_defs.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/khash.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/hts_endian.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/ksort.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/bgzf.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/thread_pool.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/klist.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/htslib/kseq.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-tiledb.a -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-tiledb.so -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/tiledb/tiledb.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_constants.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_storage.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_utils.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.a -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.1.5.4 -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.1 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.1.5.4" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb_exception.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb_status.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/include/genomicsdb_utils.h -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/genomicsdb.pc -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_demo -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_demo" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/create_genomicsdb_workspace -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/create_genomicsdb_workspace" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf2genomicsdb_init -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf2genomicsdb_init" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf2genomicsdb -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf2genomicsdb" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/consolidate_genomicsdb_array -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/consolidate_genomicsdb_array" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/gt_mpi_gather -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/gt_mpi_gather" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcfdiff -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcfdiff" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf_histogram -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/vcf_histogram" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_bcf_generator -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_bcf_generator" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_importer -- Set non-toolchain portion of runtime path of "/build/reproducible-path/genomicsdb-1.5.5/debian/tmp/usr/bin/test_genomicsdb_importer" to "/usr/lib/x86_64-linux-gnu/genomicsdb" make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu' dh_install -O--buildsystem=cmake debian/rules execute_after_dh_install-arch make[1]: Entering directory '/build/reproducible-path/genomicsdb-1.5.5' # Setting the runpath of the jni library to only contain the path to the private libs. chrpath -r "/usr/lib/x86_64-linux-gnu/genomicsdb" /build/reproducible-path/genomicsdb-1.5.5/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so /build/reproducible-path/genomicsdb-1.5.5/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so: RUNPATH=/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/src/main:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/reproducible-path/genomicsdb-1.5.5/obj-x86_64-linux-gnu/genomicsdb-htslib /build/reproducible-path/genomicsdb-1.5.5/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so: new RUNPATH: /usr/lib/x86_64-linux-gnu/genomicsdb make[1]: Leaving directory '/build/reproducible-path/genomicsdb-1.5.5' jh_installjavadoc -O--buildsystem=cmake Duplicate specification "author|A=s" for option "A" dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake jh_installlibs -O--buildsystem=cmake jh_classpath -O--buildsystem=cmake Duplicate specification "version|V" for option "V" jh_manifest -O--buildsystem=cmake Duplicate specification "version|V" for option "V" jh_exec -O--buildsystem=cmake jh_depends -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/libgenomicsdb1/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so: DWARF compression not beneficial - old size 855328 new size 870880 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: debian/libgenomicsdb1/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so contains an unresolvable reference to symbol inflateReset: it's probably a plugin dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-hts.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libgenomicsdb-tiledb.so' dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: package libgenomicsdb-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: Depends field of package libgenomicsdb-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libgenomicsdb-java' in '../libgenomicsdb-java_1.5.5-1_all.deb'. dpkg-deb: building package 'libgenomicsdb-jni' in '../libgenomicsdb-jni_1.5.5-1_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-jni-dbgsym' in '../libgenomicsdb-jni-dbgsym_1.5.5-1_amd64.deb'. dpkg-deb: building package 'genomicsdb-tools-dbgsym' in '../genomicsdb-tools-dbgsym_1.5.5-1_amd64.deb'. dpkg-deb: building package 'genomicsdb-tools' in '../genomicsdb-tools_1.5.5-1_amd64.deb'. dpkg-deb: building package 'libgenomicsdb1' in '../libgenomicsdb1_1.5.5-1_amd64.deb'. dpkg-deb: building package 'libgenomicsdb1-dbgsym' in '../libgenomicsdb1-dbgsym_1.5.5-1_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-dev' in '../libgenomicsdb-dev_1.5.5-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomicsdb_1.5.5-1_amd64.buildinfo dpkg-genchanges --build=binary -O../genomicsdb_1.5.5-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3078223/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3078223/tmp/hooks/B01_cleanup finished 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/3078223 and its subdirectories I: Current time: Thu Sep 18 14:41:28 +14 2025 I: pbuilder-time-stamp: 1758156088