I: pbuilder: network access will be disabled during build I: Current time: Mon May 8 06:45:30 +14 2023 I: pbuilder-time-stamp: 1683477930 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.4.4-3.dsc] I: copying [./genomicsdb_1.4.4.orig-genomicsdb-htslib.tar.gz] I: copying [./genomicsdb_1.4.4.orig-genomicsdb-tiledb.tar.gz] I: copying [./genomicsdb_1.4.4.orig.tar.gz] I: copying [./genomicsdb_1.4.4-3.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 27 03:44:40 2023 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomicsdb_1.4.4-3.dsc: no acceptable signature found dpkg-source: info: extracting genomicsdb in genomicsdb-1.4.4 dpkg-source: info: unpacking genomicsdb_1.4.4.orig.tar.gz dpkg-source: info: unpacking genomicsdb_1.4.4.orig-genomicsdb-htslib.tar.gz dpkg-source: info: unpacking genomicsdb_1.4.4.orig-genomicsdb-tiledb.tar.gz dpkg-source: info: unpacking genomicsdb_1.4.4-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying string_view_needs_cxx17.patch 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 JsonFormat_methods.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 spelling.patch dpkg-source: info: applying handling_rpaths.patch dpkg-source: info: applying int_type_initialization.patch dpkg-source: info: applying missing_inclusion_tiledb_constants.patch dpkg-source: info: applying using_debian_packaged_catch2.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2304883/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 May 8 06:45 /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/2304883/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2304883/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]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build 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=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6b696d014cbc4f7f806d6b9e58f65110 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=2304883 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.wZIDzfgx/pbuilderrc_NfC4 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wZIDzfgx/b2 --logfile b2/build.log --extrapackages usrmerge genomicsdb_1.4.4-3.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 8 06:45 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2304883/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), catch2, cmake, default-jdk, javahelper, libbz2-dev, libcurlpp-dev, libfmt-dev, libmuparserx-dev, libopenmpi-dev, libprotobuf-dev, libspdlog-dev, libssl-dev, liblzma-dev, maven-debian-helper, 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, libprotobuf-java-format-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 ... 19596 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 catch2; however: Package catch2 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 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 libopenmpi-dev; however: Package libopenmpi-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 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 libprotobuf-java-format-java; however: Package libprotobuf-java-format-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} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} catch2{a} chrpath{a} cmake{a} cmake-data{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} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran-12{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} ibverbs-providers{a} intltool-debian{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libarchive13{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbatik-java{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbz2-dev{a} libcairo2{a} libcbor0.8{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-compress-java{a} libcommons-configuration-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} libcups2{a} libcurl4{a} libcurl4-openssl-dev{a} libcurlpp-dev{a} libcurlpp0{a} libdatrie1{a} libdbus-1-3{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} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{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} libfmt9{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreetype6{a} libfribidi0{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-12-dev{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{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} libibverbs-dev{a} libibverbs1{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libitext1-java{a} libjansi-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjcommander-java{a} libjetty9-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjson-simple-java{a} libjsoncpp25{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm15{a} liblog4j2-java{a} libltdl-dev{a} libltdl7{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{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} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmunge2{a} libmuparserx-dev{a} libmuparserx4.0.11{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{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} libnpth0{a} libnspr4{a} libnss3{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{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} 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} libpmix-dev{a} libpmix2{a} libpng16-16{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-java-format-java{a} libprotobuf-lite32{a} libprotobuf32{a} libprotoc32{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} librdmacm1{a} libreadline8{a} libregexp-ipv6-perl{a} librhash0{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libspdlog-dev{a} libspdlog1.10{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libucx0{a} libunivocity-parsers-java{a} liburi-perl{a} libuv1{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{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} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxnvctrl0{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} ocl-icd-libopencl1{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} testng{a} unzip{a} uuid-dev{a} velocity{a} wdiff{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional bzip2-doc curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libcoarrays-openmpi-dev libdata-dump-perl libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian lynx pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace wget xauth xdg-user-dirs 0 packages upgraded, 431 newly installed, 0 to remove and 0 not upgraded. Need to get 493 MB of archives. After unpacking 1119 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.6+10-1 [43.6 MB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 catch2 amd64 2.13.10-1 [458 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.6+10-1 [168 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 169 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.6+10-1 [230 MB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 171 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.6+10-1 [4577 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 210 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.3 [1072 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B] Get: 239 http://deb.debian.org/debian bookworm/main amd64 javahelper all 0.78 [97.2 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libapiguardian-java all 1.1.2-1 [4656 B] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-java all 1.2.0-4 [9516 B] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libpicocli-java all 4.6.2-2 [390 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 junit5 all 5.9.2-1 [2398 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libbatik-java all 1.16+dfsg-1 [3908 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B] Get: 275 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 276 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 278 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 libcommons-beanutils-java all 1.9.4-1 [232 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 libcommons-configuration-java all 1.10-6 [347 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 libcommons-digester-java all 1.8.1-5 [168 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get: 297 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 298 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 299 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB] Get: 300 http://deb.debian.org/debian bookworm/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB] Get: 301 http://deb.debian.org/debian bookworm/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB] Get: 302 http://deb.debian.org/debian bookworm/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB] Get: 303 http://deb.debian.org/debian bookworm/main amd64 libcommons-text-java all 1.10.0-1 [211 kB] Get: 304 http://deb.debian.org/debian bookworm/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB] Get: 305 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-9 [487 kB] Get: 306 http://deb.debian.org/debian bookworm/main amd64 libcurlpp0 amd64 0.8.1-5 [28.3 kB] Get: 307 http://deb.debian.org/debian bookworm/main amd64 libcurlpp-dev amd64 0.8.1-5 [59.9 kB] Get: 308 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 309 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB] Get: 310 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 311 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 libfontbox2-java all 2.0.27-2 [1510 kB] Get: 314 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 315 http://deb.debian.org/debian bookworm/main amd64 libfop-java all 1:2.8-2 [10.1 MB] Get: 316 http://deb.debian.org/debian bookworm/main amd64 libitext1-java all 1.4-7 [1257 kB] Get: 317 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 318 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB] Get: 319 http://deb.debian.org/debian bookworm/main amd64 libdoxia-java all 1.12.0-1 [459 kB] Get: 320 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B] Get: 321 http://deb.debian.org/debian bookworm/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB] Get: 322 http://deb.debian.org/debian bookworm/main amd64 velocity all 1.7-6 [429 kB] Get: 323 http://deb.debian.org/debian bookworm/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB] Get: 324 http://deb.debian.org/debian bookworm/main amd64 liboro-java all 2.0.8a-14 [70.5 kB] Get: 325 http://deb.debian.org/debian bookworm/main amd64 libvelocity-tools-java all 2.0-8 [308 kB] Get: 326 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 327 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get: 328 http://deb.debian.org/debian bookworm/main amd64 libxalan2-java all 2.7.2-4 [3419 kB] Get: 329 http://deb.debian.org/debian bookworm/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB] Get: 330 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 331 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 332 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 333 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 334 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 335 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 336 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 337 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 338 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 339 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 340 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 341 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 342 http://deb.debian.org/debian bookworm/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 343 http://deb.debian.org/debian bookworm/main amd64 libfmt-dev amd64 9.1.0+ds1-2 [171 kB] Get: 344 http://deb.debian.org/debian bookworm/main amd64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get: 345 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 346 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 347 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 348 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 349 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 350 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 351 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get: 352 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-5 [153 kB] Get: 353 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB] Get: 354 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB] Get: 355 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB] Get: 356 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 357 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 358 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 359 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 360 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 361 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 362 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 363 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 364 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 365 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 366 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 367 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 368 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB] Get: 369 http://deb.debian.org/debian bookworm/main amd64 libjcommander-java all 1.71-4 [73.0 kB] Get: 370 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 371 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 372 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 373 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-3 [2962 kB] Get: 374 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 375 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 376 http://deb.debian.org/debian bookworm/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get: 377 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB] Get: 378 http://deb.debian.org/debian bookworm/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB] Get: 379 http://deb.debian.org/debian bookworm/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 380 http://deb.debian.org/debian bookworm/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 381 http://deb.debian.org/debian bookworm/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 382 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 383 http://deb.debian.org/debian bookworm/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB] Get: 384 http://deb.debian.org/debian bookworm/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB] Get: 385 http://deb.debian.org/debian bookworm/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB] Get: 386 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-incremental-java all 1.1-3 [9524 B] Get: 387 http://deb.debian.org/debian bookworm/main amd64 libplexus-compiler-java all 2.12.1-1 [99.8 kB] Get: 388 http://deb.debian.org/debian bookworm/main amd64 libqdox2-java all 2.0.3-1 [296 kB] Get: 389 http://deb.debian.org/debian bookworm/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB] Get: 390 http://deb.debian.org/debian bookworm/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB] Get: 391 http://deb.debian.org/debian bookworm/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB] Get: 392 http://deb.debian.org/debian bookworm/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB] Get: 393 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB] Get: 394 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B] Get: 395 http://deb.debian.org/debian bookworm/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB] Get: 396 http://deb.debian.org/debian bookworm/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B] Get: 397 http://deb.debian.org/debian bookworm/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB] Get: 398 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB] Get: 399 http://deb.debian.org/debian bookworm/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB] Get: 400 http://deb.debian.org/debian bookworm/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB] Get: 401 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 402 http://deb.debian.org/debian bookworm/main amd64 libmuparserx4.0.11 amd64 4.0.11-2 [192 kB] Get: 403 http://deb.debian.org/debian bookworm/main amd64 libmuparserx-dev amd64 4.0.11-2 [38.5 kB] Get: 404 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 405 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 406 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 407 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 408 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 409 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 410 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 411 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 412 http://deb.debian.org/debian bookworm/main amd64 libprotobuf32 amd64 3.21.12-3 [932 kB] Get: 413 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-lite32 amd64 3.21.12-3 [261 kB] Get: 414 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-dev amd64 3.21.12-3 [1283 kB] Get: 415 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-java all 3.21.12-3 [1257 kB] Get: 416 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-java-format-java all 1.3-1.1 [90.3 kB] Get: 417 http://deb.debian.org/debian bookworm/main amd64 libprotoc32 amd64 3.21.12-3 [829 kB] Get: 418 http://deb.debian.org/debian bookworm/main amd64 libspdlog1.10 amd64 1:1.10.0+ds-0.4 [130 kB] Get: 419 http://deb.debian.org/debian bookworm/main amd64 libspdlog-dev amd64 1:1.10.0+ds-0.4 [209 kB] Get: 420 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB] Get: 421 http://deb.debian.org/debian bookworm/main amd64 libsurefire-java all 2.22.3-2 [1169 kB] Get: 422 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B] Get: 423 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB] Get: 424 http://deb.debian.org/debian bookworm/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.2 [98.8 kB] Get: 425 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB] Get: 426 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 427 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.2 [108 kB] Get: 428 http://deb.debian.org/debian bookworm/main amd64 protobuf-compiler amd64 3.21.12-3 [83.9 kB] Get: 429 http://deb.debian.org/debian bookworm/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] Get: 430 http://deb.debian.org/debian bookworm/main amd64 testng all 6.9.12-4 [795 kB] Get: 431 http://deb.debian.org/debian bookworm/main amd64 uuid-dev amd64 2.38.1-5+b1 [39.9 kB] Fetched 493 MB in 13s (39.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20346 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package netbase. Preparing to unpack .../002-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../009-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../015-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../017-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../018-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../019-libcbor0.8_0.8.0-2+b1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../020-libfido2-1_1.12.0-2+b1_amd64.deb ... 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Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up liburi-perl (5.17-1) ... Setting up libprotobuf-java (3.21.12-3) ... Setting up chrpath (0.16-2+b1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up libprotoc32:amd64 (3.21.12-3) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libspdlog1.10:amd64 (1:1.10.0+ds-0.4) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-1) ... Setting up libdom4j-java (2.1.3-2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libjetty9-java (9.4.50-3) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up java-wrappers (0.4) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libplexus-languages-java (1.1.1-2) ... Setting up protobuf-compiler (3.21.12-3) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libmuparserx-dev:amd64 (4.0.11-2) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libmaven-parent-java (35-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libnet-http-perl (6.22-1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.16-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libprotobuf-dev:amd64 (3.21.12-3) ... Setting up libxcb-present0:amd64 (1.15-1) ... 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 (2.4.7-5) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libxalan2-java (2.7.2-4) ... Setting up testng (6.9.12-4) ... Setting up shared-mime-info (2.2-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up libfmt-dev:amd64 (9.1.0+ds1-2) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up libmaven-common-artifact-filters-java (3.3.2-1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libcommons-beanutils-java (1.9.4-1) ... Setting up libcurl4:amd64 (7.88.1-9) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libhwloc-dev:amd64 (2.9.0-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libcommons-configuration-java (1.10-6) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libxml2-utils (2.9.14+dfsg-1.2) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-5) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libcurlpp0:amd64 (0.8.1-5) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up velocity (1.7-6) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:amd64 (3.0.3+dfsg-5) ... Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libcommons-digester-java (1.8.1-5) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxmlgraphics-commons-java (2.8-2) ... Setting up libspdlog-dev:amd64 (1:1.10.0+ds-0.4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up dirmngr (2.2.40-1.1) ... Setting up libmaven-filtering-java (3.3.0-1) ... Setting up libmaven-resolver-java (1.6.3-1) ... Setting up adwaita-icon-theme (43-1) ... 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 (0.016-2) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libcurl4-openssl-dev:amd64 (7.88.1-9) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libcurlpp-dev:amd64 (0.8.1-5) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up cmake (3.25.1-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-5) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libmaven-resources-plugin-java (3.3.0-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libplexus-io-java (3.3.1-2) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libcommons-validator-java (1:1.7-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libbatik-java (1.16+dfsg-1) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libibverbs-dev:amd64 (44.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libmaven-clean-plugin-java (3.2.0-2) ... Setting up gnupg (2.2.40-1.1) ... Setting up libplexus-archiver-java (4.6.1-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libfop-java (1:2.8-2) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up libmaven-archiver-java (3.6.0-1) ... Setting up libpmix-dev:amd64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.4-3+b1) ... 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 liberror-prone-java (2.18.0-1) ... Setting up default-jre-headless (2:1.17-74) ... Setting up libwww-perl (6.68-1) ... Setting up maven-repo-helper (1.11) ... Setting up devscripts (2.23.3) ... Setting up libguava-java (31.1-1) ... Setting up ant (1.10.13-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up javahelper (0.78) ... Setting up ca-certificates-java (20230103) ... 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:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.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:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian: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_1.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:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.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 libplexus-container-default-java (2.1.1-1) ... Setting up junit4 (4.13.2-3) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up openjdk-17-jre:amd64 (17.0.6+10-1) ... Setting up default-jre (2:1.17-74) ... Setting up libmaven-antrun-plugin-java (3.1.0-1) ... Setting up libguice-java (4.2.3-2) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode 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 (1.2-3.1) ... Setting up junit5 (5.9.2-1) ... Setting up libmaven3-core-java (3.8.7-1) ... Setting up libmaven-shared-incremental-java (1.1-3) ... Setting up libmaven-shared-io-java (3.0.0-4) ... Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ... Setting up maven (3.8.7-1) ... update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode Setting up openjdk-17-jdk:amd64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ... Setting up default-jdk-headless (2:1.17-74) ... Setting up libplexus-compiler-java (2.12.1-1) ... Setting up libmaven-compiler-plugin-java (3.10.1-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ... Setting up default-jdk (2:1.17-74) ... Setting up libmaven-jar-plugin-java (3.3.0-2) ... Setting up libcommons-text-java (1.10.0-1) ... Setting up libdoxia-core-java (1.12.0-1) ... Setting up libdoxia-java (1.12.0-1) ... Setting up libmaven-reporting-api-java (3.1.1-1) ... Setting up libmaven-reporting-exec-java (1.6.0-1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up libvelocity-tools-java (2.0-8) ... Setting up libdoxia-sitetools-java (1.11.1-1) ... Setting up libmaven-site-plugin-java (3.12.1-2) ... Setting up libmaven-reporting-impl-java (3.2.0-2) ... Setting up libmaven-plugin-tools-java (3.7.1-1) ... Setting up libsurefire-java (2.22.3-2) ... Setting up maven-debian-helper (2.6.2) ... Processing triggers for ca-certificates (20230311) ... 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 (20230103) ... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/genomicsdb-1.4.4/ && 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_1.4.4-3_source.changes dpkg-buildpackage: info: source package genomicsdb dpkg-buildpackage: info: source version 1.4.4-3 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/genomicsdb-1.4.4' # Removing the files we provided manually for the build of the component if [ -e genomicsdb-htslib/CMakeLists.txt ]; then rm genomicsdb-htslib/CMakeLists.txt; fi if [ -e genomicsdb-htslib/config.h ]; then rm genomicsdb-htslib/config.h; fi if [ -e genomicsdb-htslib/version.h ]; then rm genomicsdb-htslib/version.h; fi dh_auto_clean dh_auto_clean --buildsystem=maven bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgenomicsdb-java # Removing the debian/maven.properties file we setup during configure step. if [ -e debian/maven.properties ]; then rm debian/maven.properties; fi # Removing the patched pom.xml file. if [ -e pom.xml.old ]; then mv pom.xml.old pom.xml; fi make[1]: Leaving directory '/build/genomicsdb-1.4.4' dh_autoreconf_clean -O--buildsystem=cmake jh_clean -O--buildsystem=cmake 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/genomicsdb-1.4.4' # Preparing the build of the htslib component. cp debian/htslibComponentFiles/* genomicsdb-htslib/ echo '#define HTS_VERSION_TEXT ""' > genomicsdb-htslib/version.h # Configuring the C++ part using CMake. dh_auto_configure -- \ -DBUILD_JAVA:BOOL=False \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DJAVA_HOME:PATH=/usr/lib/jvm/default-java \ -DPROTOBUF_ROOT_DIR:PATH=/usr \ -DCMAKE_LIBRARY_ARCHITECTURE:STRING=x86_64-linux-gnu \ -DVERSION=1.4.4 \ -DSOVERSION=0 cd obj-x86_64-linux-gnu && 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 -DVERSION=1.4.4 -DSOVERSION=0 .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- 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 "7.88.1") -- 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 "5.4.1") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Found libuuid: /usr/include -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.0.8") -- 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 -- Performing Test CXX_2011_FOUND -- Performing Test CXX_2011_FOUND - Success -- Compiler supports C++ 2011. -- The TileDB library is compiled with verbosity. -- 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_cxx.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) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/genomicsdb-1.4.4' debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/genomicsdb-1.4.4' # Preparing the build of the htslib component. cp debian/htslibComponentFiles/* genomicsdb-htslib/ echo '#define HTS_VERSION_TEXT ""' > genomicsdb-htslib/version.h # Configuring the C++ part using CMake. dh_auto_configure -- \ -DBUILD_JAVA:BOOL=False \ -DCMAKE_INSTALL_PREFIX:PATH=/usr \ -DJAVA_HOME:PATH=/usr/lib/jvm/default-java \ -DPROTOBUF_ROOT_DIR:PATH=/usr \ -DCMAKE_LIBRARY_ARCHITECTURE:STRING=x86_64-linux-gnu \ -DVERSION=1.4.4 \ -DSOVERSION=0 cd obj-x86_64-linux-gnu && 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 -DVERSION=1.4.4 -DSOVERSION=0 .. -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Compiler supports C++ 2011. -- The TileDB library is compiled with verbosity. -- 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) -- Configuring done -- Generating done -- Build files have been written to: /build/genomicsdb-1.4.4/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}/1.4.4/; s,\${protoc\.filepath},/usr/bin/protoc,' pom.xml.old > pom.xml dh_auto_configure --buildsystem=maven skip faking of existing gnu-getopt:getopt::debian mh_patchpoms -plibgenomicsdb-java --debian-build --keep-pom-version --maven-repo=/build/genomicsdb-1.4.4/debian/maven-repo make[1]: Leaving directory '/build/genomicsdb-1.4.4' jh_linkjars -O--buildsystem=cmake debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/genomicsdb-1.4.4' dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake --color= make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/protobuf_ep.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 0%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array.cc [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o [ 1%] Built target protobuf_ep make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_iterator.cc make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake --color= cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_read_state.cc [ 1%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_schema.cc [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/kfunc.c make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 2%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/knetfile.c make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o -MF CMakeFiles/genomicsdb-hts.dir/kstring.c.o.d -o CMakeFiles/genomicsdb-hts.dir/kstring.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/kstring.c [ 3%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_sorted_read_state.cc [ 4%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o [ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/bcf_sr_sort.c cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/array/array_sorted_write_state.cc cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/bgzf.c [ 4%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb.cc [ 5%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/errmod.c [ 5%] Generating source/header files from .proto files cd /build/genomicsdb-1.4.4/src/resources && /usr/bin/protoc --cpp_out=/build/genomicsdb-1.4.4/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 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 5%] Built target PROTOBUF_GENERATED_CXX_TARGET make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake --color= [ 5%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o -MF CMakeFiles/genomicsdb-hts.dir/faidx.c.o.d -o CMakeFiles/genomicsdb-hts.dir/faidx.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/faidx.c make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 5%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations.cc [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile.c cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o -MF CMakeFiles/genomicsdb-hts.dir/header.c.o.d -o CMakeFiles/genomicsdb-hts.dir/header.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/header.c [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc: In function 'void TileDBUtils::print_md5_hash(unsigned char*, size_t)': /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:330:6: warning: 'unsigned char* TileDBUtils::MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] 330 | MD5(buffer, length, md); | ~~~^~~~~~~~~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc:327: /usr/include/openssl/md5.h:52:38: note: declared here 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, | ^~~ /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c: In function 'libcurl_open': /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c:1335:9: warning: 'CURLINFO_CONTENT_LENGTH_DOWNLOAD' is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_libcurl.c:47: /usr/include/x86_64-linux-gnu/curl/curl.h:2858:3: note: declared here 2858 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -MF CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hfile_net.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hts.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -MF CMakeFiles/genomicsdb-hts.dir/hts_os.c.o.d -o CMakeFiles/genomicsdb-hts.dir/hts_os.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/hts_os.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o -MF CMakeFiles/genomicsdb-hts.dir/md5.c.o.d -o CMakeFiles/genomicsdb-hts.dir/md5.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/md5.c [ 7%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/multipart.c [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o -MF CMakeFiles/genomicsdb-hts.dir/probaln.c.o.d -o CMakeFiles/genomicsdb-hts.dir/probaln.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/probaln.c [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o -MF CMakeFiles/genomicsdb-hts.dir/realn.c.o.d -o CMakeFiles/genomicsdb-hts.dir/realn.c.o -c /build/genomicsdb-1.4.4/genomicsdb-htslib/realn.c [ 8%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/regidx.c [ 8%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec.cc [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/region.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/region.c [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/sam.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/sam.c [ 9%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/synced_bcf_reader.c In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/vcf_sweep.c [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/tbx.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/tbx.c [ 10%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/textutils.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/textutils.c [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/thread_pool.c [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/vcf.c [ 11%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/vcfutils.c [ 12%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_codecs.c [ 12%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_blosc.cc [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter.cc [ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_decode.c [ 13%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_bit_shuffle.cc [ 13%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_encode.c [ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_external.c [ 14%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc [ 14%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_index.c [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_gzip.cc [ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_io.c [ 15%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_lz4.cc [ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_samtools.c [ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/cram_stats.c [ 16%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_rle.cc [ 17%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/codec_zstd.cc [ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/mFILE.c [ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/open_trace_file.c [ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/pooled_alloc.c [ 18%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/bitshuffle_core.c [ 18%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/rANS_static.c [ 18%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle/iochain.c [ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/expressions/expression.cc [ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/book_keeping.cc [ 19%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/fragment.cc [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/read_state.cc [ 20%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/genomicsdb-htslib/cram/string_alloc.c [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/fragment/write_state.cc [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc [ 20%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc [ 20%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations_columnar.cc [ 20%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata_iterator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/error.cc [ 22%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'int Metadata::read(const char*, void**, size_t*)': /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:105:6: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] 105 | MD5((const unsigned char*) key, strlen(key)+1, (unsigned char*) coords); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:36: /usr/include/openssl/md5.h:52:38: note: declared here 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, | ^~~ /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc: In member function 'void Metadata::compute_array_coords(const char*, size_t, void*&, size_t&) const': /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/metadata/metadata.cc:418:8: warning: 'unsigned char* MD5(const unsigned char*, size_t, unsigned char*)' is deprecated: Since OpenSSL 3.0 [-Wdeprecated-declarations] 418 | MD5(keys_c, key_size, coords_c); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openssl/md5.h:52:38: note: declared here 52 | OSSL_DEPRECATEDIN_3_0 unsigned char *MD5(const unsigned char *d, size_t n, | ^~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/variant_operations_columnar.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/hilbert_curve.cc [ 22%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/mem_utils.cc [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/progress_bar.cc [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/uri.cc [ 23%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/misc/utils.cc [ 24%] Linking C shared library libgenomicsdb-hts.so cd /build/genomicsdb-1.4.4/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 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_buffer.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 25%] Built target genomicsdb-hts [ 25%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_fs.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/broad_combined_gvcf_columnar.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_manager.cc [ 26%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_manager_config.cc [ 26%] Building CXX object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/storage_manager/storage_posixfs.cc [ 26%] Building C object genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cc -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/storage_manager -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/bitshuffle -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4 -std=gnu11 -fPIC -MD -MT genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -MF CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o.d -o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/src/codec/external/lz4/lz4.c [ 26%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc [ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc [ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_data.cc [ 27%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_cell.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/gt_remapper_template_definition.h:25, from /build/genomicsdb-1.4.4/src/main/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_storage_manager.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_array_schema.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_array_schema.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_data.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_handler.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/query_variants.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_columnar_field.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_iterators.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc [ 29%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_text_file.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_columnar_field.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/loader/load_operators.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/query_variants.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::concatenate_field(const Variant&, const VariantQueryConfig&, unsigned int, const void**, unsigned int&) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string]': /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:724:7: note: in expansion of macro 'memcpy_s' 724 | memcpy_s(&(m_concatenation_result[curr_result_size]), vec.size()*sizeof(DataType), &(vec[0]), | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: /usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here 85 | class basic_string | ^~~~~~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc: In instantiation of 'bool VariantFieldHandler::collect_and_extend_fields(const Variant&, const VariantQueryConfig&, unsigned int, const void**, uint64_t&, bool, bool, bool) [with DataType = std::__cxx11::basic_string; CombineResultType = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:973:16: required from here /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:56:54: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 56 | #define memcpy_s(dst, dst_size, src, src_size) memcpy((dst), (src), (src_size)) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/variant_field_handler.cc:797:7: note: in expansion of macro 'memcpy_s' 797 | memcpy_s(&(m_extended_field_vector[extended_field_vector_idx]), field_ptr->length()*sizeof(DataType), | ^~~~~~~~ /usr/include/c++/12/bits/basic_string.h:85:11: note: '__gnu_cxx::__alloc_traits >, std::__cxx11::basic_string >::value_type' {aka 'class std::__cxx11::basic_string'} declared here 85 | class basic_string | ^~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_multid_vector_field.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 30%] Built target TILEDB_CORE_OBJECTS make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 30%] Linking CXX static library libgenomicsdb-tiledb.a cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -P CMakeFiles/tiledb_static.dir/cmake_clean_target.cmake cd /build/genomicsdb-1.4.4/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/ar qc libgenomicsdb-tiledb.a CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_sorted_write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/c_api/tiledb_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_blosc.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_bit_shuffle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_gzip.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_lz4.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_rle.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_zstd.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/bitshuffle_core.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/bitshuffle/iochain.c.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/expressions/expression.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/book_keeping.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/read_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/write_state.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/metadata/metadata_iterator.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/hilbert_curve.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/mem_utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/uri.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/utils.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_posixfs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/external/lz4/lz4.c.o In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/ranlib libgenomicsdb-tiledb.a make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 30%] Built target tiledb_static make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 31%] Linking CXX shared library libgenomicsdb-tiledb.so cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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_manager/storage_buffer.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_fs.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager_config.cc.o CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/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 [ 31%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/genomicsdb_importer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/loader/genomicsdb_importer.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 31%] Built target tiledb_shared make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 31%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/array/test_array_schema.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc:32: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader_file_base.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader_text_file.h:33, from /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_text_file.cc:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/loader/load_operators.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/genomicsdb-1.4.4/src/main/cpp/src/loader/genomicsdb_importer.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader_file_base.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader_file_base.cc [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/loader/tiledb_loader.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/memory_measure.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/memory_measure.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/histogram.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/histogram.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_pb.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/lut.cc [ 33%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/known_field_info.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/known_field_info.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/vid_mapper_sql.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper_sql.cc [ 34%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/timer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/timer.cc [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/genomicsdb_logger.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/genomicsdb_logger.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/known_field_info.cc:27: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/gt_common.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/known_field_info.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/known_field_info.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper.cc:33: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/vid_mapper.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/vid_mapper.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf_adapter.cc [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/genomicsdb_bcf_generator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc [ 36%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf2binary.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/alleles_combiner.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/alleles_combiner_template_definition.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc:23: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building C object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/hfile_genomicsdb.c.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cc -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/genomicsdb-1.4.4/src/main/cpp/src/vcf/hfile_genomicsdb.c [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/htslib_fs_adapter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/config/variant_query_config.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf2binary.cc:29: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/vcf2binary.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc: In function 'void* genomicsdb_filesystem_init(const char*, int)': /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc:81:13: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'TileDB_Config' {aka 'struct TileDB_Config'}; use assignment or value-initialization instead [-Wclass-memaccess] 81 | memset(&tiledb_config, 0, sizeof(TileDB_Config)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/src/vcf/htslib_fs_adapter.cc:26: /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api/tiledb.h:93:16: note: 'TileDB_Config' {aka 'struct TileDB_Config'} declared here 93 | typedef struct TileDB_Config { | ^~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/config/variant_query_config.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/genomicsdb-1.4.4/src/main/cpp/src/config/variant_query_config.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/genomicsdb_config_base.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/config/genomicsdb_config_base.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/json_config.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/config/json_config.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/pb_config.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/config/pb_config.cc [ 38%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/annotation_service.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/api/annotation_service.cc [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb.cc [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_field.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb.cc:39: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/genomicsdb-1.4.4/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/genomicsdb-1.4.4/src/main/cpp/include/api/genomicsdb.h:36, from /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb.cc:33: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_coordinates.pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_coordinates.pb.cc [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_callsets_mapping.pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_callsets_mapping.pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:39: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/genomicsdb-1.4.4/src/main/cpp/include/api/genomicsdb_exception.h:37, from /build/genomicsdb-1.4.4/src/main/cpp/include/api/genomicsdb.h:36, from /build/genomicsdb-1.4.4/src/main/cpp/include/api/genomicsdb_plink.h:35, from /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:33: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_export_config.pb.cc [ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_import_config.pb.cc /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc: In member function 'virtual void GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)': /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:366:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 366 | if(g < 0 || g >= vec.size()) { | ~~^~~~~~~~~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc: In member function 'void GenomicsDBPlinkProcessor::advance_state()': /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:653:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 653 | for(int i = 0; i < num_rows; i++) { | ~~^~~~~~~~~~ [ 41%] Building CXX object src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_vid_mapping.pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/genomicsdb_vid_mapping.pb.cc 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 42%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -MF CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d -o CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_array_schema.cc [ 42%] Linking CXX executable test_print_array_schema cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make -f genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 42%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/src/benchmark/test_print_book_keeping.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_print_book_keeping.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 42%] Built target test_print_array_schema 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 43%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/benchmark/test_sparse_array_benchmark.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 44%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc [ 45%] Linking CXX executable test_print_book_keeping cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_dense_array_api.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Built target test_print_book_keeping 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_sparse_array_api.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 45%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/c_api/test_tiledb_utils.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/codec/test_codec.cc 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/codec/test_codec_filter.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/src/expressions/test_expressions.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/expressions/test_expressions.cc 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_uri.cc make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make 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-DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc [ 48%] Linking CXX executable test_array_schema cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_array_schema.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 48%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 48%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/storage_manager/test_posixfs.cc 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 48%] Building CXX object genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_TEST_DIR=\"/build/genomicsdb-1.4.4/genomicsdb-tiledb/test\" -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/benchmark -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2 -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/array -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/c_api -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/codec -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/expressions -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/fragment -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/metadata -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/misc -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/test/../core/include/storage_manager -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/storage_manager/test_storage_buffer.cc In file included from /usr/include/c++/12/string:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:1529:21, inlined from 'GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)::&, size_t)>' at /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:625:26, inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = void; _Fn = GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)::&, size_t)>&; _Args = {const vector >&, long unsigned int}]' at /usr/include/c++/12/bits/invoke.h:61:36, inlined from 'constexpr std::enable_if_t, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = void; _Callable = GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)::&, size_t)>&; _Args = {const vector >&, long unsigned int}]' at /usr/include/c++/12/bits/invoke.h:111:28, inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)::&, size_t)>; _ArgTypes = {const std::vector >&, long unsigned int}]' at /usr/include/c++/12/bits/std_function.h:290:30: /usr/include/c++/12/bits/char_traits.h:354:14: warning: 'p' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ~~~~~^~~~~~ /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc: In static member function 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = GenomicsDBPlinkProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&, bool)::&, size_t)>; _ArgTypes = {const std::vector >&, long unsigned int}]': /build/genomicsdb-1.4.4/src/main/cpp/src/api/genomicsdb_plink.cc:606:12: note: 'p' was declared here 606 | char p; | ^ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 48%] Built target GenomicsDB_library_object_files 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 49%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/src/tiledb_array_aio_read_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_aio_read_dense.cc [ 49%] Linking CXX executable tiledb_array_aio_read_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 49%] Built target tiledb_array_aio_read_dense 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_aio_write_dense.cc [ 50%] Linking CXX executable tiledb_array_aio_write_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 50%] Built target tiledb_array_aio_write_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 50%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_consolidate.cc [ 50%] Linking CXX executable tiledb_array_consolidate cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_consolidate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 50%] Built target tiledb_array_consolidate 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 51%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/src/tiledb_array_create_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_create_dense.cc [ 51%] Linking CXX executable tiledb_array_create_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 51%] Built target tiledb_array_create_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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 51%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/src/tiledb_array_create_sparse.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_create_sparse.cc [ 52%] Linking CXX executable tiledb_array_create_sparse cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 52%] Built target tiledb_array_create_sparse 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 52%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/src/tiledb_array_iterator_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_dense.cc [ 52%] Linking CXX executable tiledb_array_iterator_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 52%] Built target tiledb_array_iterator_dense 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 53%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/src/tiledb_array_iterator_sparse.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse.cc [ 53%] Linking CXX executable tiledb_array_iterator_sparse cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 53%] Built target tiledb_array_iterator_sparse 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 53%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/src/tiledb_array_iterator_sparse_filter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse_filter.cc [ 54%] Linking CXX executable tiledb_array_iterator_sparse_filter cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 54%] Built target tiledb_array_iterator_sparse_filter 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 54%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_dense.cc [ 54%] Linking CXX executable tiledb_array_parallel_consolidate_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 54%] Built target tiledb_array_parallel_consolidate_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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 55%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_consolidate_sparse.cc [ 55%] Linking CXX executable tiledb_array_parallel_consolidate_sparse cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 55%] Built target tiledb_array_parallel_consolidate_sparse make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 55%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_1.cc [ 56%] Linking CXX executable tiledb_array_parallel_read_dense_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] Built target tiledb_array_parallel_read_dense_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_dense_2.cc [ 56%] Linking CXX executable tiledb_array_parallel_read_dense_2 cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] Built target tiledb_array_parallel_read_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_mpi_io_dense.cc In file included from /usr/include/string.h:535, from /usr/include/c++/12/cstring:42, from /usr/include/catch2/catch.hpp:5717, from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/include/catch2/catch.h:37, from /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:38: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:183:11: /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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 180 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:185:11: /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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 180 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:190:11: /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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 180 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 180 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:195:11: /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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:10: note: source object 'j' of size 8 180 | double j = 0.1, k = 0.2; | ^ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:197:11: /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/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc: In function 'void C_A_T_C_H_T_E_S_T_0()': /build/genomicsdb-1.4.4/genomicsdb-tiledb/test/src/misc/test_utils.cc:180:19: note: source object 'k' of size 8 180 | double j = 0.1, k = 0.2; | ^ [ 57%] Linking CXX executable tiledb_array_parallel_read_mpi_io_dense cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 57%] Built target tiledb_array_parallel_read_mpi_io_dense 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 57%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_1.cc [ 57%] Linking CXX executable tiledb_array_parallel_read_sparse_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 57%] Built target tiledb_array_parallel_read_sparse_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 58%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_read_sparse_2.cc [ 58%] Linking CXX executable tiledb_array_parallel_read_sparse_2 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 58%] Built target tiledb_array_parallel_read_sparse_2 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 58%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_1.cc [ 59%] Linking CXX executable tiledb_array_parallel_write_dense_1 cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 59%] Built target tiledb_array_parallel_write_dense_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 59%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_dense_2.cc [ 59%] Linking CXX executable tiledb_array_parallel_write_dense_2 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 59%] Built target tiledb_array_parallel_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 60%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_1.cc [ 60%] Linking CXX executable tiledb_array_parallel_write_sparse_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 60%] Built target tiledb_array_parallel_write_sparse_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 60%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_parallel_write_sparse_2.cc [ 61%] Linking CXX executable tiledb_array_parallel_write_sparse_2 cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 61%] Built target tiledb_array_parallel_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 61%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_primitive.cc [ 61%] Linking CXX executable tiledb_array_primitive cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_array_primitive.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 61%] Built target tiledb_array_primitive 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/src/tiledb_array_read_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_1.cc [ 62%] Linking CXX executable test_array_iterator cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx /usr/bin/ld: [ 62%] Linking CXX executable tiledb_array_read_dense_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 CMakeFiles/test_array_iterator.dir/src/c_api/test_array_iterator.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 62%] Built target tiledb_array_read_dense_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 62%] Built target test_array_iterator 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake --color= [ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/src/tiledb_array_read_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 62%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_3.cc [ 63%] Linking CXX executable tiledb_array_read_dense_2 cd /build/genomicsdb-1.4.4/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 [ 63%] Linking CXX executable tiledb_array_read_dense_3 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Built target tiledb_array_read_dense_3 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/src/tiledb_array_read_dense_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_dense_sorted.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Built target tiledb_array_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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/src/tiledb_array_read_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_1.cc [ 64%] Linking CXX executable tiledb_array_read_dense_sorted cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 64%] Linking CXX executable tiledb_array_read_sparse_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 64%] Linking CXX executable test_tiledb_utils cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tiledb_utils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx /usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 64%] Built target tiledb_array_read_dense_sorted 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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/src/tiledb_array_read_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Built target tiledb_array_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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' CMakeFiles/test_tiledb_utils.dir/src/c_api/test_tiledb_utils.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/src/tiledb_array_read_sparse_filter_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_1.cc [ 65%] Linking CXX executable tiledb_array_read_sparse_2 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Built target test_tiledb_utils 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 65%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_2.cc [ 65%] Linking CXX executable test_sparse_array_benchmark [ 66%] Linking CXX executable tiledb_array_read_sparse_filter_1 cd /build/genomicsdb-1.4.4/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 cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx [ 66%] Linking CXX executable test_codec cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 66%] Built target tiledb_array_read_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 66%] Linking CXX executable tiledb_array_read_sparse_filter_2 cd /build/genomicsdb-1.4.4/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 [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/src/tiledb_array_read_sparse_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_sorted.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/ld: [ 67%] Linking CXX executable tiledb_array_read_sparse_sorted cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 CMakeFiles/test_sparse_array_benchmark.dir/src/benchmark/test_sparse_array_benchmark.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Built target tiledb_array_read_sparse_filter_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Linking CXX executable test_dense_array_api [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/src/tiledb_array_update_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_1.cc cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Built target test_codec 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/src/tiledb_array_update_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 67%] Built target tiledb_array_read_sparse_filter_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/DependInfo.cmake --color= [ 67%] Built target tiledb_array_read_sparse_sorted 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake --color= /usr/bin/ld: make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -MF CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o.d -o CMakeFiles/tiledb_array_update_sparse_1.dir/src/tiledb_array_update_sparse_1.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_1.cc [ 68%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/src/tiledb_array_update_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_update_sparse_2.cc [ 69%] Linking CXX executable tiledb_array_update_dense_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 CMakeFiles/test_dense_array_api.dir/src/c_api/test_dense_array_api.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 69%] Linking CXX executable tiledb_array_update_dense_2 cd /build/genomicsdb-1.4.4/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 [ 70%] Linking CXX executable tiledb_array_update_sparse_2 cd /build/genomicsdb-1.4.4/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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 70%] Built target test_sparse_array_benchmark make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 70%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/src/tiledb_array_write_dense_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc [ 70%] Linking CXX executable tiledb_array_update_sparse_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 70%] Built target test_dense_array_api 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 71%] Linking CXX executable test_array_schema_api cd /build/genomicsdb-1.4.4/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 [ 71%] Built target tiledb_array_update_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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 71%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/src/tiledb_array_write_dense_sorted.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_dense_sorted.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 71%] Linking CXX executable tiledb_array_write_dense_1 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 71%] Built target tiledb_array_update_dense_2 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/ld: [ 72%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_1.cc [ 73%] Linking CXX executable test_mem_utils cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mem_utils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_update_sparse_2 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/src/tiledb_array_write_sparse_2.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_2.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_update_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/src/tiledb_array_write_sparse_3.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_3.cc CMakeFiles/test_array_schema_api.dir/src/c_api/test_array_schema_api.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 73%] Linking CXX executable tiledb_array_write_dense_2 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/tiledb_array_write_dense_2.dir/src/tiledb_array_write_dense_2.cc.o -o tiledb_array_write_dense_2 ../core/libgenomicsdb-tiledb.a /usr/lib/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 [ 73%] Linking CXX executable tiledb_array_write_dense_sorted cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 74%] Linking CXX executable test_codec_filter cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_codec_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx [ 74%] Linking CXX executable test_uri cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_uri.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 74%] Built target test_mem_utils 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 75%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/src/tiledb_array_write_sparse_4.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_array_write_sparse_4.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 76%] Linking CXX executable tiledb_array_write_sparse_2 cd /build/genomicsdb-1.4.4/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 [ 76%] Built target tiledb_array_write_dense_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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_catching_errors.cc [ 76%] Linking CXX executable tiledb_array_write_sparse_1 cd /build/genomicsdb-1.4.4/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 [ 76%] Linking CXX executable tiledb_array_write_sparse_3 cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 76%] Built target test_codec_filter make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 76%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_clear_delete_move.cc [ 76%] Built target test_array_schema_api make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/src/tiledb_config.cc.o make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_config.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 77%] Built target tiledb_array_write_dense_sorted make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/depend [ 77%] Built target test_uri make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend [ 77%] Built target tiledb_array_write_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build [ 77%] Linking CXX executable tiledb_array_write_sparse_4 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build [ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_delete.cc make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 77%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_ls.cc [ 78%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_ls_workspaces.cc [ 79%] Linking CXX executable tiledb_catching_errors cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_catching_errors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Built target tiledb_array_write_sparse_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_consolidate.cc [ 79%] Linking CXX executable tiledb_config cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_config.dir/link.txt --verbose=1 [ 79%] Linking CXX executable tiledb_clear_delete_move cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 79%] Built target tiledb_array_write_sparse_3 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Built target tiledb_array_write_sparse_4 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/DependInfo.cmake --color= [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/src/tiledb_metadata_create.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_create.cc [ 79%] Linking CXX executable tiledb_ls_workspaces cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls_workspaces.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Linking CXX executable tiledb_ls cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_ls.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_iterator.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Built target tiledb_array_write_sparse_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_primitive.cc [ 80%] Linking CXX executable tiledb_metadata_consolidate cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_consolidate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 81%] Linking CXX executable tiledb_delete cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_delete.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 82%] Linking CXX executable tiledb_metadata_iterator cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_iterator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 82%] Built target tiledb_catching_errors 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -MD -MT genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -MF CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d -o CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o -c /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_read.cc [ 83%] Linking CXX executable tiledb_metadata_primitive cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 83%] Linking CXX executable tiledb_metadata_create cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledb_metadata_create.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 [ 83%] Built target tiledb_config make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Built target tiledb_clear_delete_move make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_update.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_metadata_write.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Built target tiledb_metadata_consolidate 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Building CXX object genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/src/tiledb_workspace_group_create.cc.o [ 83%] Built target tiledb_ls cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples && /usr/bin/c++ -DENABLE_ZSTD -DHAVE_OPENMP -DTILEDB_VERBOSE -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/usr/include/muparserx -I/build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/../core/include/c_api -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -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/genomicsdb-1.4.4/genomicsdb-tiledb/examples/src/tiledb_workspace_group_create.cc make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Built target tiledb_ls_workspaces make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend [ 83%] Linking CXX shared library libgenomicsdb.so cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/tiledbgenomicsdb.dir/link.txt --verbose=1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake --color= /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 -shared -Wl,-soname,libgenomicsdb.so.0 -o libgenomicsdb.so.1.4.4 CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/variant_operations_columnar.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/broad_combined_gvcf_columnar.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/query_operations/gt_remapper_gvcf_columnar_iterator.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_cell.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_field_data.cc.o CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_array_schema.cc.o 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directory '/build/genomicsdb-1.4.4/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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f 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-I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas 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-I/build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/tools/src/vcf2genomicsdb.cc cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/tools/src/vcfdiff.cc cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/cmake -E cmake_symlink_library libgenomicsdb.so.1.4.4 libgenomicsdb.so.0 libgenomicsdb.so make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 87%] Built target tiledbgenomicsdb make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 88%] Building CXX object tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/tools/src/vcf_histogram.cc [ 89%] Linking CXX executable create_genomicsdb_workspace cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o -o create_genomicsdb_workspace -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 89%] Built target create_genomicsdb_workspace make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/tools/include -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/tools/include/vcfdiff.h:31, from /build/genomicsdb-1.4.4/tools/src/vcfdiff.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, from /build/genomicsdb-1.4.4/tools/src/vcfdiff.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/tools/src/gt_mpi_gather.cc:30: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/tools/src/gt_mpi_gather.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 90%] Linking CXX executable test_utils cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_utils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx /usr/bin/ld: CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/tools/src/vcf2genomicsdb.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/genomicsdb-1.4.4/tools/src/vcf2genomicsdb.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/genomicsdb-1.4.4/tools/src/vcf_histogram.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 90%] Built target test_utils make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 90%] Building CXX object example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:28: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/tools/src/consolidate_genomicsdb_array.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:28: /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In member function 'virtual void OneQueryIntervalProcessor::process(const std::string&, const int64_t*, const genomic_interval_t&, const std::vector&)': /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:296:37: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 296 | CHECK(genomic_fields.size() == m_attributes_size + 2); // Add '2' for REF and ALT fields | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_bcf_generator.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc: In function 'void C_A_T_C_H_T_E_S_T_40()': /build/genomicsdb-1.4.4/src/test/cpp/src/test_genomicsdb_api.cc:589:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 589 | CHECK(num_threads == threads.size()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [ 90%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc [ 90%] Linking CXX executable test_sparse_array_api cd /build/genomicsdb-1.4.4/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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx /usr/bin/ld: CMakeFiles/test_sparse_array_api.dir/src/c_api/test_sparse_array_api.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 90%] Built target test_sparse_array_api make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:26: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/catch2/catch.hpp:477, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_non_diploid_mapper.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/example/src/test_genomicsdb_importer.cc [ 92%] Linking CXX executable test_storage_buffer cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_storage_buffer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx /usr/bin/ld: CMakeFiles/test_storage_buffer.dir/src/storage_manager/test_storage_buffer.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' [ 92%] Linking CXX executable test_genomicsdb_bcf_generator cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o -o test_genomicsdb_bcf_generator -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl [ 92%] Linking CXX executable test_posixfs cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_posixfs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o -o test_posixfs ../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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 92%] Built target test_storage_buffer make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBUtils.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc /usr/bin/ld: CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o: in function `TempDir::create_temp_directory()': ./obj-x86_64-linux-gnu/genomicsdb-tiledb/test/./genomicsdb-tiledb/test/include/catch2/catch.h:99: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 92%] Built target test_posixfs [ 92%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc [ 92%] Linking CXX executable gt_mpi_gather cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o -o gt_mpi_gather -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:28: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api/tiledb.h:43, from /build/genomicsdb-1.4.4/genomicsdb-tiledb/core/include/c_api/tiledb_utils.h:38, from /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBUtils.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 92%] Built target test_genomicsdb_bcf_generator [ 93%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQuery.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/genomicsdb_importer.h:25, from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_importer.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/example/src/test_genomicsdb_importer.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Linking CXX executable vcfdiff cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdiff.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o -o vcfdiff -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 94%] Built target gt_mpi_gather [ 94%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQueryStream.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 94%] Built target vcfdiff [ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_multid_vector.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_multid_vector.cc [ 95%] Building CXX object src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -Dgenomicsdbjni_EXPORTS -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -I/build/genomicsdb-1.4.4/src/main/jni/include -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_jni_init.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/load_operators.h:27, from /build/genomicsdb-1.4.4/src/main/cpp/include/loader/tiledb_loader.h:29, from /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:24: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/vcf2binary.h:26, from /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBImporter.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_pb.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/variant_operations.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/query_operations/broad_combined_gvcf.h:26, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:27, from /build/genomicsdb-1.4.4/src/main/jni/src/genomicsdb_GenomicsDBQueryStream.cc:25: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/genomicsdb-1.4.4/src/main/cpp/include/utils/headers.h:30, from /build/genomicsdb-1.4.4/src/main/cpp/include/vcf/genomicsdb_bcf_generator.h:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_logger.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_field_data.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_multid_vector_field.h:27, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_multid_vector.cc:27: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/catch2/catch.hpp:477, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_multid_vector.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc In file included from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_iterators.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_cell.h:28, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/variant_storage_manager.h:29, from /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/query_variants.h:27, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:30: /build/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb/genomicsdb_columnar_field.h:290:10: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 290 | : std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/catch2/catch.hpp:477, from /build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_htslib_plugin.cc /build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc: In function 'void C_A_T_C_H_T_E_S_T_2()': /build/genomicsdb-1.4.4/src/test/cpp/src/test_columnar_gvcf_iterator.cc:390:59: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint64_t' {aka 'long unsigned int'} [-Wsign-compare] 390 | REQUIRE(bcf_hdr_nsamples(bag.hdr[GoldTestEnum::GOLD]) == query_config.get_num_rows_to_query()); [ 96%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_alleles_combiner.cc [ 97%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_gt_remapper.cc [ 97%] Linking CXX executable vcf_histogram cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf_histogram.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o -o vcf_histogram -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl [ 97%] Linking CXX executable consolidate_genomicsdb_array cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/consolidate_genomicsdb_array.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o -o consolidate_genomicsdb_array -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl [ 97%] Building CXX object src/test/cpp/CMakeFiles/ctests.dir/src/test_bgen.cc.o cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/c++ -DDUPLICATE_CELL_AT_END=1 -DFMT_SHARED -DGENOMICSDB_CTESTS_DIR=\"/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/\" -DGENOMICSDB_TESTS_SRC_DIR=\"/build/genomicsdb-1.4.4/tests/\" -DGENOMICSDB_VERSION=\"1.4.4-SNAPSHOT-\" -DINCLUDE_TEST_BGEN=1 -DSTRING_VIEW_FOUND=1 -D_FILE_OFFSET_BITS=64 -I/build/genomicsdb-1.4.4/genomicsdb-htslib -I/build/genomicsdb-1.4.4/genomicsdb-tiledb -I/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/src/main/cpp/include/genomicsdb -I/build/genomicsdb-1.4.4/src/main/cpp/include/loader -I/build/genomicsdb-1.4.4/src/main/cpp/include/query_operations -I/build/genomicsdb-1.4.4/src/main/cpp/include/utils -I/build/genomicsdb-1.4.4/src/main/cpp/include/vcf -I/build/genomicsdb-1.4.4/src/main/cpp/include/config -I/build/genomicsdb-1.4.4/src/main/cpp/include/api -I/build/genomicsdb-1.4.4/src/test/cpp/include -I/build/genomicsdb-1.4.4/src/test/cpp/Catch -I/build/genomicsdb-1.4.4/src/test/cpp/INTERFACE -I/build/genomicsdb-1.4.4/src/test/cpp/Catch2/single_include -I/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources -g -O2 -ffile-prefix-map=/build/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fstack-protector-strong -Wall -Wno-reorder -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-result -fopenmp -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/genomicsdb-1.4.4/src/test/cpp/src/test_bgen.cc [ 98%] Linking CXX executable test_expressions cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -Wno-literal-suffix -fopenmp -Wl,-z,relro -Wl,-z,now 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 -ldl -lmuparserx make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 98%] Built target vcf_histogram make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 98%] Built target test_expressions make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 98%] Built target consolidate_genomicsdb_array [ 99%] Linking CXX executable vcf2genomicsdb cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o -o vcf2genomicsdb -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 99%] Built target vcf2genomicsdb [ 99%] Linking CXX executable test_genomicsdb_importer cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o -o test_genomicsdb_importer -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl [ 99%] Linking CXX executable vcf2genomicsdb_init cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o -o vcf2genomicsdb_init -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 99%] Built target vcf2genomicsdb_init make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 99%] Built target test_genomicsdb_importer [100%] Linking CXX shared library libgenomicsdbjni.so cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 -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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib libgenomicsdb.so.1.4.4 ../../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_cxx.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.9.1.0 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [100%] Built target genomicsdbjni [100%] Linking CXX executable api_tests cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp && /usr/bin/cmake -E tar xzf /build/genomicsdb-1.4.4/src/test/cpp/../inputs/test.tgz make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [100%] Built target api_tests [100%] Linking CXX executable ctests cd /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -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 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 -o ctests -Wl,-rpath,/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/build/genomicsdb-1.4.4/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_cxx.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/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.9.1.0 /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/libssl.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libuuid.so -ldl make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [100%] Built target ctests make[3]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/genomicsdb-1.4.4' debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/genomicsdb-1.4.4' # Building the Java part with Maven. dh_auto_build --buildsystem=maven /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/genomicsdb-1.4.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/genomicsdb-1.4.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/genomicsdb-1.4.4/debian -Dmaven.repo.local=/build/genomicsdb-1.4.4/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.genomicsdb:genomicsdb:jar:1.4.4 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 235, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] [INFO] ---------------------< org.genomicsdb:genomicsdb >---------------------- [INFO] Building org.genomicsdb:genomicsdb 1.4.4 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0 [WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0 [WARNING] The artifact com.googlecode.json-simple:json-simple:jar:debian has been relocated to com.github.cliftonlabs:json-simple:jar:debian [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-protoc) @ genomicsdb --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/genomicsdb-1.4.4/build/src/main/java [INFO] Executed tasks [INFO] [INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-source) @ genomicsdb --- [INFO] Source directory: /build/genomicsdb-1.4.4/build/src/main/java added. [INFO] Source directory: /build/genomicsdb-1.4.4/src/main/java added. [INFO] Source directory: /build/genomicsdb-1.4.4/src/main/scala added. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ genomicsdb --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ genomicsdb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 30 source files to /build/genomicsdb-1.4.4/build/classes [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[483,84] PARSER in org.genomicsdb.model.Coordinates.GenomicsDBColumnOrInterval has been deprecated [WARNING] /build/genomicsdb-1.4.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7297,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,50] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[176,28] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[351,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[351,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[352,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[352,30] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[354,9] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[354,41] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[356,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[356,36] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[360,17] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[360,40] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[480,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[480,45] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[501,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[501,41] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/extensions/VidMapExtensions.java:[253,55] unchecked conversion required: java.util.List found: java.util.ArrayList [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,32] unchecked method invocation: method jniQueryVariantCalls in class org.genomicsdb.reader.GenomicsDBQuery is applied to given types required: long,java.lang.String,java.util.List,java.util.List found: long,java.lang.String,java.util.List,java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,63] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,87] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,32] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,32] unchecked method invocation: method jniQueryVariantCalls in class org.genomicsdb.reader.GenomicsDBQuery is applied to given types required: long,java.lang.String,java.util.List,java.util.List found: long,java.lang.String,java.util.List,java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,77] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,32] unchecked conversion required: java.util.List found: java.util.List [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/genomicsdb-1.4.4/src/test/resources [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (unzip-test-artifacts) @ genomicsdb --- [INFO] Executing tasks [INFO] [mkdir] Created dir: /build/genomicsdb-1.4.4/build/test [INFO] [copy] Copying 1 file to /build/genomicsdb-1.4.4/build/test [INFO] [gunzip] Expanding test.tar.gz to /build/genomicsdb-1.4.4/build/test/test.tar [INFO] [untar] Expanding: /build/genomicsdb-1.4.4/build/test/test.tar into /build/genomicsdb-1.4.4/build/test [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ genomicsdb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 12 source files to /build/genomicsdb-1.4.4/build/test-classes [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/GenomicsDBUtilsTest.java:[36,24] createTempDir() in com.google.common.io.Files has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/model/ImportConfigSpec.java:[65,43] unchecked conversion required: java.util.Set found: java.util.HashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[104,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[119,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[133,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,38] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,13] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,39] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,44] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[195,18] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[252,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[283,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[315,76] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[354,81] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[390,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[434,81] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[473,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[526,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ genomicsdb --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ genomicsdb --- [INFO] Building jar: /build/genomicsdb-1.4.4/build/genomicsdb-1.4.4.jar [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 39.619 s [INFO] Finished at: 2023-05-08T07:03:05+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/genomicsdb-1.4.4' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/genomicsdb-1.4.4' dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles/protobuf_ep.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/DependInfo.cmake --color= 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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/bgzf.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f CMakeFiles/protobuf_ep.dir/build.make CMakeFiles/protobuf_ep.dir/build Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/protobuf_ep.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". 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Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/array/array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/array/array_sorted_read_state.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/array/array_sorted_write_state.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/c_api/tiledb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". [ 0%] Built target protobuf_ep Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/c_api/tiledb_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/depend Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/errmod.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_blosc.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/faidx.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_filter_bit_shuffle.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/header.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_filter_delta_encode.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_gzip.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_lz4.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/codec_zstd.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/hts_os.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kfunc.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/knetfile.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/kstring.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/fragment/book_keeping.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/md5.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/multipart.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/fragment/fragment.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make -f src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build.make src/resources/CMakeFiles/PROTOBUF_GENERATED_CXX_TARGET.dir/build Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/probaln.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/fragment/read_state.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/realn.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/regidx.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/fragment/write_state.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/metadata/metadata.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". Dependencies file "genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/vcf.c.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/metadata/metadata_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". [ 0%] Built target PROTOBUF_GENERATED_CXX_TARGET Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/error.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/hilbert_curve.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make -f src/main/CMakeFiles/GenomicsDB_library_object_files.dir/build.make src/main/CMakeFiles/GenomicsDB_library_object_files.dir/depend Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/misc/progress_bar.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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_manager/storage_buffer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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_manager/storage_fs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/storage_manager/storage_manager.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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[4]: Leaving directory '/build/genomicsdb-1.4.4/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/storage_manager/storage_manager_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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_manager/storage_posixfs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target TILEDB_CORE_OBJECTS Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_export_config.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/__/resources/genomicsdb_import_config.pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". [ 13%] Built target genomicsdb-hts Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_field.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/api/genomicsdb_plink.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". [ 25%] Built target TILEDB_CORE_OBJECTS make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_static.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/config/variant_query_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/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/genomicsdb/genomicsdb_multid_vector_field.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core /build/genomicsdb-1.4.4/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/genomicsdb/variant.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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_cell.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build.make genomicsdb-tiledb/core/CMakeFiles/tiledb_shared.dir/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/genomicsdb/variant_storage_manager.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/load_operators.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/build Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/loader/tiledb_loader.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". [ 25%] Built target tiledb_static 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". 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Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/utils/lut.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/depend Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf2binary.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/DependInfo.cmake --color= Dependencies file "src/main/CMakeFiles/GenomicsDB_library_object_files.dir/cpp/src/vcf/vcf_adapter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/GenomicsDB_library_object_files.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/src/array/test_array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/compiler_depend.internal". 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target test_array_schema make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema.dir/build Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/src/benchmark/test_print_array_schema.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_array_schema.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_print_array_schema 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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.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/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_print_book_keeping.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_print_book_keeping 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_benchmark.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_sparse_array_benchmark Consolidate compiler generated dependencies of target test_array_iterator make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/compiler_depend.internal". [ 27%] Built target test_array_schema make -f genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_iterator.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_array_schema_api make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 28%] Built target test_print_array_schema 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_dense_array_api make -f genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_array_schema_api.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_dense_array_api.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target GenomicsDB_library_object_files make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 [ 29%] Built target test_print_book_keeping [ 30%] Built target test_sparse_array_benchmark [ 31%] Built target test_array_iterator [ 31%] Built target test_array_schema_api 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/depend [ 31%] Built target test_dense_array_api make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/depend 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_sparse_array_api.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/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 Consolidate compiler generated dependencies of target test_sparse_array_api make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/src/codec/test_codec.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_tiledb_utils Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/src/codec/test_codec_filter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_tiledb_utils.dir/build Consolidate compiler generated dependencies of target test_codec Consolidate compiler generated dependencies of target test_codec_filter make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_expressions make -f genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_codec.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_codec_filter.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Built target GenomicsDB_library_object_files Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/src/misc/test_mem_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_expressions.dir/build Consolidate compiler generated dependencies of target test_mem_utils make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/test/CMakeFiles/test_mem_utils.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 46%] Built target test_sparse_array_api make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/depend [ 46%] Built target test_tiledb_utils [ 47%] Built target test_codec_filter make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/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 [ 48%] Built target test_codec [ 49%] Built target test_expressions make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/depend [ 50%] Built target test_mem_utils make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/DependInfo.cmake --color= 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_uri.dir/src/misc/test_uri.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/depend Consolidate compiler generated dependencies of target test_uri Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/src/misc/test_utils.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/src/storage_manager/test_posixfs.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_utils make -f genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_uri.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target test_posixfs make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/compiler_depend.internal". make -f genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_utils.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/src/tiledb_array_consolidate.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_consolidate.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_storage_buffer make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_posixfs.dir/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_read_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_aio_write_dense.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_aio_read_dense make -f genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build.make genomicsdb-tiledb/test/CMakeFiles/test_storage_buffer.dir/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_consolidate Consolidate compiler generated dependencies of target tiledb_array_aio_write_dense make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_create_dense make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 50%] Built target test_utils [ 51%] Built target test_uri [ 51%] Built target test_posixfs [ 52%] Built target test_storage_buffer [ 53%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.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 [ 54%] Built target tiledb_array_aio_write_dense make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/DependInfo.cmake --color= 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/DependInfo.cmake --color= 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 [ 55%] Built target tiledb_array_create_dense 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/DependInfo.cmake --color= 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 Consolidate compiler generated dependencies of target tiledb_array_create_sparse [ 55%] Built target tiledb_array_consolidate make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_iterator_dense make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_create_sparse.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_iterator_sparse_filter.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_iterator_sparse_filter make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/src/tiledb_array_parallel_consolidate_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/compiler_depend.internal". 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 Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_dense make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_dense.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 56%] Built target tiledb_array_create_sparse [ 56%] Built target tiledb_array_iterator_dense make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/DependInfo.cmake --color= 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 [ 57%] Built target tiledb_array_iterator_sparse make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.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 [ 57%] Built target tiledb_array_parallel_consolidate_dense [ 58%] Built target tiledb_array_iterator_sparse_filter make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_read_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/depend Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/src/tiledb_array_parallel_read_dense_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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_consolidate_sparse.dir/src/tiledb_array_parallel_consolidate_sparse.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_1 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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_parallel_read_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_1.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_1.dir/build Consolidate compiler generated dependencies of target tiledb_array_parallel_consolidate_sparse make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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 make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_dense_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_consolidate_sparse.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_sparse_2.dir/src/tiledb_array_parallel_read_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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_mpi_io_dense.dir/src/tiledb_array_parallel_read_mpi_io_dense.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_read_mpi_io_dense.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_read_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_parallel_read_mpi_io_dense 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/genomicsdb-1.4.4/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 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 [ 59%] Built target tiledb_array_parallel_read_dense_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 59%] Built target tiledb_array_parallel_read_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/depend [ 59%] Built target tiledb_array_parallel_read_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/DependInfo.cmake --color= [ 60%] Built target tiledb_array_parallel_read_mpi_io_dense [ 61%] Built target tiledb_array_parallel_consolidate_sparse 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 [ 62%] Built target tiledb_array_parallel_read_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/DependInfo.cmake --color= 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 -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/DependInfo.cmake --color= [ 63%] Built target tiledb_array_parallel_write_dense_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_parallel_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_dense_2.dir/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/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/src/tiledb_array_parallel_write_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/src/tiledb_array_parallel_write_sparse_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/DependInfo.cmake --color= Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_primitive.dir/src/tiledb_array_primitive.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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_write_sparse_2 Consolidate compiler generated dependencies of target tiledb_array_parallel_write_sparse_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_primitive make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_parallel_write_sparse_2.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_dense_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_2 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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/src/tiledb_array_read_dense_3.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_3.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_3 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 63%] Built target tiledb_array_parallel_write_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 -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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 64%] Built target tiledb_array_parallel_write_sparse_2 [ 65%] Built target tiledb_array_parallel_write_sparse_1 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/depend [ 66%] Built target tiledb_array_read_dense_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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/DependInfo.cmake --color= [ 67%] Built target tiledb_array_read_dense_2 [ 67%] Built target tiledb_array_primitive make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/depend [ 67%] Built target tiledb_array_read_dense_3 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_1.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/depend make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/DependInfo.cmake --color= 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_read_dense_sorted 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_read_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_dense_sorted.dir/build Consolidate compiler generated dependencies of target tiledb_array_read_sparse_2 make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/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_1.dir/src/tiledb_array_read_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_1.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/src/tiledb_array_read_sparse_filter_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_read_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/depend Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_1 Consolidate compiler generated dependencies of target tiledb_array_read_sparse_filter_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_sorted.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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_read_sparse_sorted [ 68%] Built target tiledb_array_read_dense_sorted 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 [ 69%] Built target tiledb_array_read_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_read_sparse_filter_2.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/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_2.dir/src/tiledb_array_update_dense_2.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_update_dense_1 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_update_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_1.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_dense_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 69%] Built target tiledb_array_read_sparse_1 [ 70%] Built target tiledb_array_read_sparse_filter_1 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 [ 70%] Built target tiledb_array_read_sparse_filter_2 [ 71%] Built target tiledb_array_read_sparse_sorted make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/depend [ 72%] Built target tiledb_array_update_dense_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_dense_sorted.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/depend [ 72%] Built target tiledb_array_update_dense_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/depend 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/DependInfo.cmake --color= Consolidate compiler generated dependencies of target tiledb_array_update_sparse_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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_update_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_1.dir/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_dense_1 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_dense_2 make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/depend make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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_dense_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_1.dir/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_update_sparse_2 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_update_sparse_2.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/src/tiledb_array_write_sparse_1.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_2.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_sparse_1 make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_array_write_sparse_2 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_dense_sorted.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build Consolidate compiler generated dependencies of target tiledb_array_write_dense_sorted make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_1.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_array_write_sparse_3 make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_update_sparse_1 make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_3.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 73%] Built target tiledb_array_write_dense_1 [ 74%] Built target tiledb_array_update_sparse_2 [ 75%] Built target tiledb_array_write_dense_2 [ 76%] Built target tiledb_array_write_sparse_1 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 [ 76%] Built target tiledb_array_write_dense_sorted make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/DependInfo.cmake --color= 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/depend [ 76%] Built target tiledb_array_write_sparse_3 [ 77%] Built target tiledb_array_write_sparse_2 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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 Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/src/tiledb_catching_errors.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/depend Consolidate compiler generated dependencies of target tiledb_catching_errors make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_catching_errors.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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_clear_delete_move.dir/src/tiledb_clear_delete_move.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_clear_delete_move Consolidate compiler generated dependencies of target tiledb_array_write_sparse_4 make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.dir/src/tiledb_delete.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_delete.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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.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 Consolidate compiler generated dependencies of target tiledb_delete make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_config make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_clear_delete_move.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_array_write_sparse_4.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build [ 78%] Built target tiledb_catching_errors Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/src/tiledb_ls.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_ls make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_config.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls.dir/build Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/src/tiledb_ls_workspaces.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_ls_workspaces make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_ls_workspaces.dir/build [ 78%] Built target tiledb_clear_delete_move make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 79%] Built target tiledb_array_write_sparse_4 [ 80%] Built target tiledb_delete make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/depend [ 81%] Built target tiledb_config make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/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 [ 81%] Built target tiledb_ls make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.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 [ 82%] Built target tiledb_ls_workspaces make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.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_metadata_consolidate.dir/src/tiledb_metadata_consolidate.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_metadata_consolidate make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/DependInfo.cmake --color= 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_metadata_create.dir/src/tiledb_metadata_create.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_create make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/src/tiledb_metadata_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_iterator.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/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 Consolidate compiler generated dependencies of target tiledb_metadata_iterator make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_consolidate.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/src/tiledb_metadata_primitive.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_primitive.dir/compiler_depend.internal". Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/src/tiledb_metadata_read.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_metadata_read Consolidate compiler generated dependencies of target tiledb_metadata_primitive make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_create.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/src/tiledb_metadata_update.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/compiler_depend.internal". make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_read.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target tiledb_metadata_update make[4]: Leaving directory '/build/genomicsdb-1.4.4/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[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_update.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 83%] Built target tiledb_metadata_consolidate [ 83%] Built target tiledb_metadata_create [ 84%] Built target tiledb_metadata_iterator make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/depend [ 84%] Built target tiledb_metadata_primitive make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/DependInfo.cmake --color= make -f genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/build.make genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/DependInfo.cmake --color= [ 85%] Built target tiledb_metadata_read make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/tiledbgenomicsdb.dir/DependInfo.cmake --color= make -f src/main/CMakeFiles/genomicsdb.dir/build.make src/main/CMakeFiles/genomicsdb.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdb.dir/DependInfo.cmake --color= [ 86%] Built target tiledb_metadata_update Dependencies file "genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/src/tiledb_metadata_write.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_metadata_write.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target tiledb_metadata_write make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/main/CMakeFiles/tiledbgenomicsdb.dir/build.make src/main/CMakeFiles/tiledbgenomicsdb.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples/CMakeFiles/tiledb_workspace_group_create.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/tiledbgenomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/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 Consolidate compiler generated dependencies of target tiledb_workspace_group_create make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 86%] Built target tiledbgenomicsdb make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/depend [ 86%] Built target tiledb_metadata_write make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/DependInfo.cmake --color= [ 87%] Built target tiledb_workspace_group_create [ 88%] 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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/DependInfo.cmake --color= make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/depend Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBImporter.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_GenomicsDBQuery.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". Dependencies file "src/main/CMakeFiles/genomicsdbjni.dir/jni/src/genomicsdb_jni_init.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main/CMakeFiles/genomicsdbjni.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/depend Consolidate compiler generated dependencies of target genomicsdbjni make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/DependInfo.cmake --color= make -f src/main/CMakeFiles/genomicsdbjni.dir/build.make src/main/CMakeFiles/genomicsdbjni.dir/build Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/ctest_main.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/depend Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_alleles_combiner.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_columnar_gvcf_iterator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_config.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_gt_remapper.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/api_tests.dir/src/test_genomicsdb_api.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/api_tests.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target api_tests make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/DependInfo.cmake --color= make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/depend Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_htslib_plugin.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_logger.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/DependInfo.cmake --color= Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_non_diploid_mapper.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". Dependencies file "src/test/cpp/CMakeFiles/ctests.dir/src/test_pb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/CMakeFiles/ctests.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/depend Dependencies file "tools/CMakeFiles/create_genomicsdb_workspace.dir/src/create_genomicsdb_workspace.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/create_genomicsdb_workspace.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/DependInfo.cmake --color= make -f src/test/cpp/CMakeFiles/api_tests.dir/build.make src/test/cpp/CMakeFiles/api_tests.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/main/CMakeFiles/genomicsdbjni.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Dependencies file "tools/CMakeFiles/gt_mpi_gather.dir/src/gt_mpi_gather.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/gt_mpi_gather.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target create_genomicsdb_workspace Consolidate compiler generated dependencies of target gt_mpi_gather Dependencies file "tools/CMakeFiles/vcf2genomicsdb_init.dir/src/vcf2genomicsdb_init.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb_init.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target vcf2genomicsdb_init make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/api_tests.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/create_genomicsdb_workspace.dir/build.make tools/CMakeFiles/create_genomicsdb_workspace.dir/build make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target ctests Dependencies file "tools/CMakeFiles/vcf2genomicsdb.dir/src/vcf2genomicsdb.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf2genomicsdb.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/create_genomicsdb_workspace.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f src/test/cpp/CMakeFiles/ctests.dir/build.make src/test/cpp/CMakeFiles/ctests.dir/build Dependencies file "tools/CMakeFiles/vcfdiff.dir/src/vcfdiff.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcfdiff.dir/compiler_depend.internal". make -f tools/CMakeFiles/gt_mpi_gather.dir/build.make tools/CMakeFiles/gt_mpi_gather.dir/build Consolidate compiler generated dependencies of target vcfdiff make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf2genomicsdb_init.dir/build.make tools/CMakeFiles/vcf2genomicsdb_init.dir/build Consolidate compiler generated dependencies of target vcf2genomicsdb Dependencies file "tools/CMakeFiles/vcf_histogram.dir/src/vcf_histogram.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/vcf_histogram.dir/compiler_depend.internal". make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target vcf_histogram make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/gt_mpi_gather.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 90%] Built target genomicsdbjni make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'src/test/cpp/CMakeFiles/ctests.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf2genomicsdb.dir/build.make tools/CMakeFiles/vcf2genomicsdb.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb_init.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcfdiff.dir/build.make tools/CMakeFiles/vcfdiff.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf2genomicsdb.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/vcf_histogram.dir/build.make tools/CMakeFiles/vcf_histogram.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcfdiff.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/vcf_histogram.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 91%] Built target create_genomicsdb_workspace [ 92%] Built target api_tests [ 92%] Built target gt_mpi_gather [ 95%] Built target ctests [ 95%] Built target vcf2genomicsdb_init make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/depend [ 96%] Built target vcf2genomicsdb make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/DependInfo.cmake --color= make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/depend make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/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 [ 97%] Built target vcfdiff [ 98%] Built target vcf_histogram make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' cd /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/genomicsdb-1.4.4 /build/genomicsdb-1.4.4/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/DependInfo.cmake --color= Dependencies file "tools/CMakeFiles/consolidate_genomicsdb_array.dir/src/consolidate_genomicsdb_array.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools/CMakeFiles/consolidate_genomicsdb_array.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target consolidate_genomicsdb_array make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f tools/CMakeFiles/consolidate_genomicsdb_array.dir/build.make tools/CMakeFiles/consolidate_genomicsdb_array.dir/build Dependencies file "example/CMakeFiles/test_genomicsdb_bcf_generator.dir/src/test_genomicsdb_bcf_generator.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_bcf_generator.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target test_genomicsdb_bcf_generator Dependencies file "example/CMakeFiles/test_genomicsdb_importer.dir/src/test_genomicsdb_importer.cc.o.d" is newer than depends file "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/example/CMakeFiles/test_genomicsdb_importer.dir/compiler_depend.internal". make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'tools/CMakeFiles/consolidate_genomicsdb_array.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build.make example/CMakeFiles/test_genomicsdb_bcf_generator.dir/build Consolidate compiler generated dependencies of target test_genomicsdb_importer make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make -f example/CMakeFiles/test_genomicsdb_importer.dir/build.make example/CMakeFiles/test_genomicsdb_importer.dir/build make[4]: Entering directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 99%] Built target consolidate_genomicsdb_array make[4]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'example/CMakeFiles/test_genomicsdb_importer.dir/build'. make[4]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' [ 99%] Built target test_genomicsdb_bcf_generator [100%] Built target test_genomicsdb_importer make[3]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/genomicsdb-1.4.4/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/genomicsdb-1.4.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/genomicsdb-1.4.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/genomicsdb-1.4.4/debian -Dmaven.repo.local=/build/genomicsdb-1.4.4/debian/maven-repo --batch-mode test OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release. [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.genomicsdb:genomicsdb:jar:1.4.4 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 235, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] [INFO] ---------------------< org.genomicsdb:genomicsdb >---------------------- [INFO] Building org.genomicsdb:genomicsdb 1.4.4 [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0 [WARNING] The artifact com.googlecode.json-simple:json-simple:jar:debian has been relocated to com.github.cliftonlabs:json-simple:jar:debian [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (exec-protoc) @ genomicsdb --- [INFO] Executing tasks [INFO] Executed tasks [INFO] [INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-source) @ genomicsdb --- [INFO] Source directory: /build/genomicsdb-1.4.4/build/src/main/java added. [INFO] Source directory: /build/genomicsdb-1.4.4/src/main/java added. [INFO] Source directory: /build/genomicsdb-1.4.4/src/main/scala added. [INFO] [INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ genomicsdb --- [INFO] Copying 0 resource [INFO] [INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ genomicsdb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 30 source files to /build/genomicsdb-1.4.4/build/classes [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[48,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[49,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[50,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[51,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[483,84] PARSER in org.genomicsdb.model.Coordinates.GenomicsDBColumnOrInterval has been deprecated [WARNING] /build/genomicsdb-1.4.4/build/src/main/java/org/genomicsdb/model/GenomicsDBExportConfiguration.java:[7297,72] PARSER in org.genomicsdb.model.Coordinates.ContigInterval has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[107,50] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[176,28] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[340,73] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[351,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[351,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[352,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[352,30] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[354,9] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[354,41] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[356,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[356,36] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[360,17] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[360,40] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[385,44] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[480,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[480,45] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[501,9] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[501,41] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/GenomicsDBImporter.java:[816,58] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/importer/extensions/VidMapExtensions.java:[253,55] unchecked conversion required: java.util.List found: java.util.ArrayList [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,32] unchecked method invocation: method jniQueryVariantCalls in class org.genomicsdb.reader.GenomicsDBQuery is applied to given types required: long,java.lang.String,java.util.List,java.util.List found: long,java.lang.String,java.util.List,java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,63] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,87] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[174,32] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,32] unchecked method invocation: method jniQueryVariantCalls in class org.genomicsdb.reader.GenomicsDBQuery is applied to given types required: long,java.lang.String,java.util.List,java.util.List found: long,java.lang.String,java.util.List,java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,77] unchecked conversion required: java.util.List found: java.util.List [WARNING] /build/genomicsdb-1.4.4/src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java:[180,32] unchecked conversion required: java.util.List found: java.util.List [INFO] [INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ genomicsdb --- [INFO] skip non existing resourceDirectory /build/genomicsdb-1.4.4/src/test/resources [INFO] [INFO] --- maven-antrun-plugin:3.1.0:run (unzip-test-artifacts) @ genomicsdb --- [INFO] Executing tasks [INFO] [untar] Expanding: /build/genomicsdb-1.4.4/build/test/test.tar into /build/genomicsdb-1.4.4/build/test [INFO] Executed tasks [INFO] [INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ genomicsdb --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 12 source files to /build/genomicsdb-1.4.4/build/test-classes [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[52,23] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[53,23] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[54,30] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[55,30] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/GenomicsDBUtilsTest.java:[36,24] createTempDir() in com.google.common.io.Files has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/model/ImportConfigSpec.java:[65,43] unchecked conversion required: java.util.Set found: java.util.HashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[104,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[119,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[133,43] unchecked conversion required: java.util.Set found: java.util.LinkedHashSet [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,9] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[171,33] org.json.simple.parser.JSONParser in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,13] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[175,38] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,13] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[176,39] org.json.simple.JSONArray in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,17] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[181,44] org.json.simple.JSONObject in org.json.simple has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[195,18] org.json.simple.parser.ParseException in org.json.simple.parser has been deprecated [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[252,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[283,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[315,76] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[354,81] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[390,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[434,81] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[473,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [WARNING] /build/genomicsdb-1.4.4/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[526,79] unchecked conversion required: htsjdk.tribble.CloseableTribbleIterator found: htsjdk.tribble.CloseableTribbleIterator [INFO] [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ genomicsdb --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB GenomicsDB: org.genomicsdb.importer.extensions.VidMapExtensions VCF header has 2 lines with the same field name test_field and header line type -- only the first line is considered by GenomicsDB ERROR StatusLogger Reconfiguration failed: No configuration found for '5cb0d902' at 'null' in 'null' GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.022234489,Cpu time(s),0.007869442999999999 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.015472890999999999,Cpu time(s),0.004209475 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001363761,Cpu time(s),0.00138309 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.001214896,Cpu time(s),0.0010651249999999999 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.011077613,Cpu time(s),0.0029441349999999996 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.25071E-4,Cpu time(s),7.25301E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),6.43591E-4,Cpu time(s),5.17754E-4 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),0.013192113,Cpu time(s),0.001362287 [INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 51.192 s - in TestSuite [INFO] [INFO] Results: [INFO] [INFO] Tests run: 44, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:32 min [INFO] Finished at: 2023-05-08T07:04:54+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/genomicsdb-1.4.4' dh_auto_test -O--buildsystem=cmake -Nlibgenomicsdb-java cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 make[1]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j15 UpdateCTestConfiguration from :/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/genomicsdb-1.4.4/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 test 1 Start 1: test_array_schema 1: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_schema 1: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_print_array_schema 2: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_print_book_keeping 3: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_benchmark 4: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_iterator 5: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_array_schema_api 6: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_dense_array_api 7: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_sparse_array_api 8: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_tiledb_utils 9: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_codec 10: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_codec_filter 11: Working Directory: /build/genomicsdb-1.4.4/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/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_expressions 12: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 12: Test timeout computed to be: 10000000 test 13 Start 13: test_mem_utils 13: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_mem_utils 13: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 13: Test timeout computed to be: 10000000 test 14 Start 14: test_uri 14: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_uri 14: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 14: Test timeout computed to be: 10000000 test 15 Start 15: test_utils 15: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_utils 15: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 15: Test timeout computed to be: 10000000 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/genomicsdb-1.4.4/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: =============================================================================== 4: test cases: 1 | 1 passed 4: assertions: - none - 4: 5: =============================================================================== 5: All tests passed (527 assertions in 6 test cases) 5: 6: =============================================================================== 6: All tests passed (335 assertions in 13 test cases) 6: 9: [TileDB::utils] Error: (set_working_dir) Failed to set_working_dir as /tmp/TileDBTestl9esv0/WORKSPACE.non-existent does not exist 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestGJdmUa/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=/tmp/TileDBTestGJdmUa/WORKSPACE errno=2(No such file or directory) 9: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=/tmp/TileDBTestQDXClN/WORKSPACE errno=2(No such file or directory) 9: 7e820c3ee657b1a27a56a7be9d202a7a7e820c3ee657b1a27a56a7be9d202a7a[TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTest1Es64O/test_file 9: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTest1Es64O/test_file 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: [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: [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. 13: Mon May 8 07:04:56 2023 Memory stats Tracking memory usage START size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 14: =============================================================================== 14: All tests passed (58 assertions in 1 test case) 14: 1/21 Test #1: test_array_schema ................ Passed 0.27 sec test 16 Start 16: test_posixfs 16: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_posixfs 16: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 16: Test timeout computed to be: 10000000 2/21 Test #2: test_print_array_schema .......... Passed 0.27 sec test 17 Start 17: test_storage_buffer 17: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test/test_storage_buffer 17: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/test 17: Test timeout computed to be: 10000000 3/21 Test #3: test_print_book_keeping .......... Passed 0.27 sec test 18 Start 18: ci_tests 18: Test command: /build/genomicsdb-1.4.4/genomicsdb-tiledb/examples/run_examples.sh 18: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/examples 18: Test timeout computed to be: 10000000 4/21 Test #4: test_sparse_array_benchmark ...... Passed 0.26 sec test 19 Start 19: ctests 19: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests "-d" "yes" 19: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp 19: Test timeout computed to be: 10000000 5/21 Test #5: test_array_iterator .............. Passed 0.26 sec test 20 Start 20: api_tests 20: Test command: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/api_tests "-d" "yes" 20: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp 20: Test timeout computed to be: 10000000 6/21 Test #6: test_array_schema_api ............ Passed 0.27 sec test 21 Start 21: tools_tests 21: Test command: /build/genomicsdb-1.4.4/tests/test_tools.sh "/build/genomicsdb-1.4.4/tests/inputs/vcfs" "/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools" 21: Working Directory: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/tools 21: Test timeout computed to be: 10000000 7/21 Test #10: test_codec ....................... Passed 0.22 sec 8/21 Test #11: test_codec_filter ................ Passed 0.21 sec 9/21 Test #14: test_uri ......................... Passed 0.16 sec 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: (Expression) Attribute a2 in expression filter not present in the array schema 12: [TileDB::Expression] Error: (evaluate_cell) Parser evaluate error, possibly due to bad filter expression: 12: Undefined token "a2" found at position 0. 15: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; invalid input buffer format 15: [TileDB::utils] Error: (RLE_compress) Failed compressing with RLE; output buffer overflow 15: [TileDB::utils] Error: (RLE_compress_coords_row) Failed compressing coordinates with RLE; invalid buffer format 15: [TileDB::utils] Error: (RLE_compress_coords_row) Filed compressing coordinates with RLE; output buffer overflow 15: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; invalid buffer format 15: [TileDB::utils] Error: (RLE_compress_coords_col) Failed compressing coordinates with RLE; output buffer overflow 15: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/dir errno=2(No such file or directory) 15: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/non-existent-dir/file errno=2(No such file or directory) 15: [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) 15: [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) 15: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/non-existent-dir/file errno=2(No such file or directory) 15: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=/non-existent-dir/dir errno=2(No such file or directory) 15: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=/non-existent-dir/old errno=2(No such file or directory) 15: =============================================================================== 15: All tests passed (86 assertions in 6 test cases) 15: 10/21 Test #15: test_utils ....................... Passed 0.14 sec 16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory; Directory already exists path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir 16: [TileDB::FileSystem] Error: (create_dir) Cannot create directory path=/non-existent-dir/foo errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir errno=21(Is a directory) 16: [TileDB::FileSystem] Error: (create_file) Failed to create file path=/tmp/TileDBTestBMdo04/test_posixfs_dirdir errno=21(Is a directory) 16: [TileDB::FileSystem] Error: (get_dirs) Cannot open directory path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (move_path) Cannot rename path path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (delete_dir) Could not recursively delete directory path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (get_files) Cannot open directory path=non-existent-dir errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (delete_file) Cannot remove file path=/tmp/TileDBTestqiPgQ8/test_posixfs_dirfile/foo1 errno=2(No such file or directory) 16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo 16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo 16: [TileDB::FileSystem] Error: (read_from_file) EOF reached; File reading error path=/tmp/TileDBTestinE5vy/test_posixfs_dirread_write/foo 16: [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) 16: [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) 16: [TileDB::FileSystem] Error: (read_from_file) Cannot open simultaneously for reads/writes path=test_posixfs_dir_locking/foo 16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_sync 16: [TileDB::FileSystem] Error: (~PosixFS) File does not seem to be closed path=test_dir_locking1/foo_no_close 16: =============================================================================== 16: All tests passed (258 assertions in 11 test cases) 16: 11/21 Test #16: test_posixfs ..................... Passed 0.13 sec 17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestLuoCaC/test-file 17: [TileDB::StorageBuffer] Error: (StorageBuffer) File does not seem to exist or is of zero length path=/tmp/TileDBTestLuoCaC/test-file-non-existent errno=2(No such file or directory) 17: [TileDB::StorageBuffer] Error: (StorageBuffer) Cannot perform buffered reads or writes as there is no buffer chunk size set path=/tmp/TileDBTestLuoCaC/test-file 17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTestLuoCaC/test-file 17: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied) 17: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (gzip_write_buffer) Cannot write bytes path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (write_buffer) Cannot compress and/or write bytes path=/non-existent-file errno=13(Permission denied) 17: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=13(Permission denied) 17: [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) 17: [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) 17: [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) 17: [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) 17: [TileDB::StorageBuffer] Error: (write_buffer) Compression type=1000 not supported in StorageBuffer 17: [TileDB::StorageBuffer] Error: (finalize) Could not finalize buffer after compression path=/non-existent-file errno=2(No such file or directory) 17: [TileDB::StorageBuffer] Error: (read_buffer) Compression type=1000 for read_buffer not supported for CompressedStorageBuffer 17: [TileDB::StorageBuffer] Error: (read_buffer) Cannot read past the filesize from buffer path=/tmp/TileDBTests7F4l5/compressed_foo 18: Example 1: Running ./tiledb_workspace_group_create... 18: Example 1: Done running ./tiledb_workspace_group_create 18: Example 2: Running ./tiledb_ls_workspaces... 12: [TileDB::Expression] Error: (Expression) Expression parsing for dense arrays not yet implemented 12: =============================================================================== 12: All tests passed (3009 assertions in 80 test cases) 12: 12/21 Test #12: test_expressions ................. Passed 0.24 sec 20: 0.000 s: api get_version 20: 0.000 s: api empty_args 18: my_workspace 18: Example 2: Done running ./tiledb_ls_workspaces 18: Example 3: Running ./tiledb_array_create_dense... 19: 0.017 s: Check loader configuration with json file 19: 0.001 s: Check configuration with json file 19: 0.001 s: Check configuration with json file and shared posifs optim 19: 0.001 s: Compare configuration with json file and string 19: 0.000 s: genotype_ordering haploid_5_alleles 19: 0.000 s: genotype_ordering diploid_2_alleles 19: 0.000 s: genotype_ordering diploid_3_alleles 19: 0.000 s: genotype_ordering diploid_4_alleles 19: 0.000 s: genotype_ordering triploid_2_alleles 19: 0.000 s: genotype_ordering triploid_3_alleles 19: 0.000 s: genotype_ordering triploid_4_alleles 19: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles 19: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF 19: 0.000 s: multid_vector 2D_test 19: 0.000 s: multid_vector 3D_test 19: 0.000 s: multid_vector 2D_test_with_missing_values 19: 0.000 s: multid_vector 2D_float_test 19: 0.000 s: multid_vector 2D_tuple_test 19: 0.000 s: pb_query_config_test 18: Example 3: Done running ./tiledb_array_create_dense 18: Example 4: Running ./tiledb_array_create_sparse... 19: 0.019 s: pb_vid_mapping_test 19: 07:04:56.475 INFO NativeGenomicsDB - pid=2673112 tid=2673112 This is a test 19: 07:04:56.475 WARN NativeGenomicsDB - pid=2673112 tid=2673112 This is a test 19: 07:04:56.475 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 This is a test 19: 07:04:56.475 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 This is a test 19: This is a test 19: This is a test 19: This is a test 19: This is a test 19: This is a once_only test 19: Trying format Hello1 Hello2 19: 0.000 s: test logger 19: 07:04:56.476 INFO NativeGenomicsDB - pid=2673112 tid=2673112 i=1 str=This is a test 19: 07:04:56.476 WARN NativeGenomicsDB - pid=2673112 tid=2673112 i=2 str=This is a test 19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 i=3 str=This is a test 19: 07:04:56.476 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 i=4 str=This is a test 19: 07:04:56.476 INFO NativeGenomicsDB - pid=2673112 tid=2673112 i=6 str=This is a once_only test 19: 07:04:56.476 WARN NativeGenomicsDB - pid=2673112 tid=2673112 i=7 str=This is a once_only test 19: 0.000 s: test logger format 19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 i=1 str=This is a test 19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception 19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception 19: 07:04:56.476 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception 19: 07:04:56.489 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Native Stack Trace: 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2e6) [0x55f9e86392e6] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] 19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] 19: 07:04:56.490 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Test Exception 19: 07:04:56.490 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 Native Stack Trace: 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeb2f6) [0x55f9e86392f6] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] 19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] 19: 0.014 s: test logger exceptions 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea6e) [0x55f9e863ca6e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] 19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xf745e) [0x55f9e864545e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0xeea81) [0x55f9e863ca81] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x6cf2d) [0x55f9e85baf2d] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x85d28) [0x55f9e85d3d28] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8c923) [0x55f9e85da923] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ea0e) [0x55f9e85dca0e] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x8ef2a) [0x55f9e85dcf2a] 19: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/ctests(+0x5fce9) [0x55f9e85adce9] 19: /lib/x86_64-linux-gnu/libc.so.6(+0x2718a) [0x7fa98b58318a] 19: This is a test 19: 0.000 s: test explicit logger 18: Example 4: Done running ./tiledb_array_create_sparse 18: Example 5: Running ./tiledb_array_primitive... 18: Array name: my_workspace/dense_arrays/my_array_A 18: Attributes: a1 a2 a3 18: The array is dense 18: Array name: my_workspace/sparse_arrays/my_array_B 18: Attributes: a1 a2 a3 18: The array is sparse 19: 0.112 s: gvcf iterator 18: Example 5: Done running ./tiledb_array_primitive 20: 0.224 s: api query_variants direct DP 18: Example 6: Running ./tiledb_array_write_dense_1... 19: 0.087 s: columnar_gvcf_iterator_test 19: [TileDB] Error: No TileDB support for URL=dfdfd://ddd. 19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 htslib_plugin could not open file dfdfd://ddd No TileDB support for URL=dfdfd://ddd 19: [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) 19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 hts_plugin read /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) 19: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory) 19: 07:04:56.690 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 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) 19: 0.001 s: test htslib plugin 19: 0.000 s: alleles_combiner 19: 0.000 s: gt_remapper 20: 0.067 s: api query_variants direct DP with huge row range 18: Example 6: Done running ./tiledb_array_write_dense_1 18: Example 7: Running ./tiledb_array_write_sparse_1... 20: 0.069 s: api query_variants direct DP with huge disjoint row ranges 18: Example 7: Done running ./tiledb_array_write_sparse_1 20: 0.120 s: api query_variants direct DP with range composed of multiple points 20: 0.139 s: api query_variants direct DP with range composed of overlapping ranges 20: 0.034 s: api query_variants direct DP with invalid row range 13: Mon May 8 07:04:57 2023 Memory stats Tracking memory usage END size=6MB resident=3MB share=3MB text=404KB lib=0 data=528KB dt=0 13: =============================================================================== 13: test cases: 1 | 1 passed 13: assertions: - none - 13: 13/21 Test #13: test_mem_utils ................... Passed 1.02 sec 20: 0.205 s: api query_variants direct DP and GT 20: 0.206 s: api query_variants direct DP and GT with PP 20: 0.153 s: api query_variants with json 20: /build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/test/cpp/inputs/ws/t0_1_2/.__consolidation_lock 20: 0.137 s: api query variants with json string 20: 0.067 s: api query variants with enabled shared posixfs optimizations 20: ---------------- 20: Interval:[0,1000000000] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] DP:76 20: 0.222 s: api query_variant_calls direct 20: ---------------- 20: Interval:[0,1000000000] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] GT:1/1 DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 20: 0.220 s: api query_variant_calls direct DP and GT 20: ---------------- 20: Interval:[0,1000000000] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] GT:0|0 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] GT:1/1 DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 20: 0.219 s: api query_variant_calls direct DP and GT with PP 20: ---------------- 20: Interval:[0,1000000000] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] DP:76 20: 0.107 s: api query_variant_calls with json 9: =============================================================================== 9: All tests passed (10488234 assertions in 9 test cases) 9: 20: ---------------- 20: Interval:[0,1000000000] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] GT:1/1 DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 14/21 Test #9: test_tiledb_utils ................ Passed 2.52 sec 20: ---------------- 20: Interval:[0,249250620] 20: 20: sample=HG00141 20: row=0 position=12140 20: genomic_interval=1:12141,12295 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG01958 20: row=1 position=12144 20: genomic_interval=1:12145,12277 20: genomic_fields 20: REF:C ALT:[] GT:0/0 20: sample=HG00141 20: row=0 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 20: sample=HG01958 20: row=1 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[T, ] GT:1/1 DP:120 20: sample=HG01530 20: row=2 position=17384 20: genomic_interval=1:17385,17385 20: genomic_fields 20: REF:G ALT:[A, ] GT:0/1 DP:76 20: 0.107 s: api query_variant_calls with protobuf 20: 0.220 s: api generate_vcf direct 20: 0.069 s: api generate_vcf with json 20: 1.988 s: api generate_vcf with json multiple threads 20: ---------------- 20: Interval:[0,1000000000] 20: 20: ---------------- 20: Interval:[0,1000000000] 20: 20: 0.069 s: api annotate query_variant_calls with test datasource 0 20: =============================================================================== 20: All tests passed (731 assertions in 22 test cases) 20: 15/21 Test #20: api_tests ........................ Passed 4.80 sec 18: Example 8: Running ./tiledb_ls... 18: my_workspace WORKSPACE 18: Example 8: Done running ./tiledb_ls 18: Example 9: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 8 i ( 8.1, 8.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 11 llll ( 11.1, 11.2) 18: 12 m ( 12.1, 12.2) 18: 13 nn ( 13.1, 13.2) 18: 14 ooo ( 14.1, 14.2) 18: 15 pppp ( 15.1, 15.2) 18: Example 9: Done running ./tiledb_array_read_dense_1 18: Example 10: Running ./tiledb_array_write_dense_2... 18: Example 10: Done running ./tiledb_array_write_dense_2 19: 07:05:03.686 INFO NativeGenomicsDB - pid=2673112 tid=2673112 Plink progress 3452039 / 6904084 = 50.00% 19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12277 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] 19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12277 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] 19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] 19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] 19: 07:05:03.693 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG01958 row: 1 column: 12299 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG01958 row: 1 column: 12299 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG00141 row: 0 column: 12399 contains a negative value or otherwise did not parse, full string: [-2147483648, -2147483648, -2147483648] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG00141 row: 0 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 PL field for sample: HG01958 row: 1 column: 12399 contains a negative value or otherwise did not parse, full string: [0, 1, -2147483648] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 GL field for sample: HG01958 row: 1 column: 12399 contains a strictly positive value or otherwise did not parse, full string [nan, nan, nan] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 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] 19: 07:05:03.694 ERROR NativeGenomicsDB - pid=2673112 tid=2673112 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] 19: 07:05:03.694 WARN NativeGenomicsDB - pid=2673112 tid=2673112 GL probabilities at sample: HG01958 row: 1 column: 12499 sum to 0.8981071705534972, expected near 1. Generated BGEN may be invalid 19: 7.050 s: test bgen 19: =============================================================================== 19: All tests passed (1425 assertions in 30 test cases) 19: 19: 07:05:03.740 DEBUG NativeGenomicsDB - pid=2673112 tid=2673112 Deleting htslib_fs_adapter tiledb_ctx_map 16/21 Test #19: ctests ........................... Passed 7.60 sec 17: +++ we are here 2 17: =============================================================================== 17: All tests passed (450703 assertions in 3 test cases) 17: 17/21 Test #17: test_storage_buffer .............. Passed 8.93 sec 18: Example 11: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 8 i ( 8.1, 8.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 11 llll ( 11.1, 11.2) 18: 12 m ( 12.1, 12.2) 18: 13 nn ( 13.1, 13.2) 18: 14 ooo ( 14.1, 14.2) 18: 15 pppp ( 15.1, 15.2) 18: Example 11: Done running ./tiledb_array_read_dense_1 18: Example 12: Running ./tiledb_array_read_dense_2... 18: a1 18: ---- 18: Reading cells... 18: 9 18: 11 18: 12 18: Reading cells... 18: 13 18: 14 18: 15 18: Example 12: Done running ./tiledb_array_read_dense_2 18: Example 13: Running ./tiledb_array_write_dense_sorted... 18: Example 13: Done running ./tiledb_array_write_dense_sorted 18: Example 14: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 8 i ( 8.1, 8.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 11 llll ( 11.1, 11.2) 18: 12 m ( 12.1, 12.2) 18: 13 nn ( 13.1, 13.2) 18: 14 ooo ( 14.1, 14.2) 18: 15 pppp ( 15.1, 15.2) 18: Example 14: Done running ./tiledb_array_read_dense_1 18: Example 15: Running ./tiledb_array_update_dense_1... 18: Example 15: Done running ./tiledb_array_update_dense_1 8: 10% [=== ] 20% [====== ] 30% [========= ] 40% [============ ] 50% [=============== ] 60% [================== ] 70% [===================== ] 80% [======================= ] 89% [========================== ] 99% [============================= ] =============================================================================== 8: All tests passed (15200383 assertions in 14 test cases) 8: 18/21 Test #8: test_sparse_array_api ............ Passed 20.67 sec 18: Example 16: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 8 i ( 8.1, 8.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 11 llll ( 11.1, 11.2) 18: 112 M (112.1, 112.2) 18: 113 NN (113.1, 113.2) 18: 114 OOO (114.1, 114.2) 18: 115 PPPP (115.1, 115.2) 18: Example 16: Done running ./tiledb_array_read_dense_1 18: Example 17: Running ./tiledb_array_update_dense_2... 18: Example 17: Done running ./tiledb_array_update_dense_2 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 (109505881 assertions in 4 test cases) 7: 19/21 Test #7: test_dense_array_api ............. Passed 23.45 sec 18: Example 18: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 208 u (208.1, 208.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 211 wwww (211.1, 211.2) 18: 212 x (212.1, 212.2) 18: 213 yy (213.1, 213.2) 18: 114 OOO (114.1, 114.2) 18: 115 PPPP (115.1, 115.2) 18: Example 18: Done running ./tiledb_array_read_dense_1 18: Example 19: Running ./tiledb_array_write_sparse_1... 18: Example 19: Done running ./tiledb_array_write_sparse_1 18: Example 20: Running ./tiledb_array_read_sparse_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: (1, 1) 0 a ( 0.1, 0.2) 18: (1, 2) 1 bb ( 1.1, 1.2) 18: (1, 4) 2 ccc ( 2.1, 2.2) 18: (2, 3) 3 dddd ( 3.1, 3.2) 18: (3, 1) 4 e ( 4.1, 4.2) 18: (4, 2) 5 ff ( 5.1, 5.2) 18: (3, 3) 6 ggg ( 6.1, 6.2) 18: (3, 4) 7 hhhh ( 7.1, 7.2) 18: Example 20: Done running ./tiledb_array_read_sparse_1 18: Example 21: Running ./tiledb_array_read_sparse_filter_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: Example 21: Done running ./tiledb_array_read_sparse_filter_1 18: Example 22: Running ./tiledb_array_iterator_sparse... 18: a1 18: ---- 18: 5 18: 6 18: 7 18: Example 22: Done running ./tiledb_array_iterator_sparse 18: Example 23: Running ./tiledb_array_iterator_sparse_filter... 18: a1 18: ---- 18: 6 18: 7 18: Example 23: Done running ./tiledb_array_iterator_sparse_filter 18: Example 24: Running ./tiledb_array_read_sparse_2... 18: a1 18: ---- 18: Reading cells... 18: 5 18: 6 18: Reading cells... 18: 7 18: Example 24: Done running ./tiledb_array_read_sparse_2 18: Example 25: Running ./tiledb_array_read_sparse_filter_2... 18: a1 18: ---- 18: Reading cells... 18: 6 18: Reading cells... 18: 7 18: Example 25: Done running ./tiledb_array_read_sparse_filter_2 18: Example 26: Running ./tiledb_array_write_sparse_2... 18: Example 26: Done running ./tiledb_array_write_sparse_2 18: Example 27: Running ./tiledb_array_read_sparse_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: (1, 1) 0 a ( 0.1, 0.2) 18: (1, 2) 1 bb ( 1.1, 1.2) 18: (1, 4) 2 ccc ( 2.1, 2.2) 18: (2, 3) 3 dddd ( 3.1, 3.2) 18: (3, 1) 4 e ( 4.1, 4.2) 18: (4, 2) 5 ff ( 5.1, 5.2) 18: (3, 3) 6 ggg ( 6.1, 6.2) 18: (3, 4) 7 hhhh ( 7.1, 7.2) 18: Example 27: Done running ./tiledb_array_read_sparse_1 18: Example 28: Running ./tiledb_array_read_sparse_2... 18: a1 18: ---- 18: Reading cells... 18: 5 18: 6 18: Reading cells... 18: 7 18: Example 28: Done running ./tiledb_array_read_sparse_2 18: Example 29: Running ./tiledb_array_read_sparse_filter_2... 18: a1 18: ---- 18: Reading cells... 18: 6 18: Reading cells... 18: 7 18: Example 29: Done running ./tiledb_array_read_sparse_filter_2 18: Example 30: Running ./tiledb_array_update_sparse_1... 18: Example 30: Done running ./tiledb_array_update_sparse_1 18: Example 31: Running ./tiledb_array_read_sparse_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: (1, 1) 0 a ( 0.1, 0.2) 18: (1, 2) 1 bb ( 1.1, 1.2) 18: (1, 4) 2 ccc ( 2.1, 2.2) 18: (2, 3) 3 dddd ( 3.1, 3.2) 18: (3, 1) 4 e ( 4.1, 4.2) 18: (3, 2) 104 u (104.1, 104.2) 18: (4, 1) 105 vvvv (105.1, 105.2) 18: (4, 2) 5 ff ( 5.1, 5.2) 18: (3, 3) 106 w (106.1, 106.2) 18: (3, 4) 107 yyy (107.1, 107.2) 18: Example 31: Done running ./tiledb_array_read_sparse_1 18: Example 32: Running ./tiledb_array_read_sparse_filter_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: (4, 1) 105 vvvv (105.1, 105.2) 18: Example 32: Done running ./tiledb_array_read_sparse_filter_1 18: Example 33: Running ./tiledb_array_read_sparse_filter_2... 18: a1 18: ---- 18: Reading cells... 18: Reading cells... 18: 106 18: 107 18: Example 33: Done running ./tiledb_array_read_sparse_filter_2 18: Example 34: Running ./tiledb_array_iterator_sparse... 18: a1 18: ---- 18: 104 18: 5 18: 106 18: 107 18: Example 34: Done running ./tiledb_array_iterator_sparse 18: Example 35: Running ./tiledb_array_iterator_sparse_filter... 18: a1 18: ---- 18: 104 18: 106 18: 107 18: Example 35: Done running ./tiledb_array_iterator_sparse_filter 18: Example 36: Running ./tiledb_array_read_sparse_2... 18: a1 18: ---- 18: Reading cells... 18: 104 18: 5 18: Reading cells... 18: 106 18: 107 18: Example 36: Done running ./tiledb_array_read_sparse_2 18: Example 37: Running ./tiledb_array_consolidate... 18: Example 37: Done running ./tiledb_array_consolidate 18: Example 38: Running ./tiledb_array_read_dense_1... 18: a1 a2 (a3.first, a3.second) 18: ----------------------------------------- 18: 0 a ( 0.1, 0.2) 18: 1 bb ( 1.1, 1.2) 18: 2 ccc ( 2.1, 2.2) 18: 3 dddd ( 3.1, 3.2) 18: 4 e ( 4.1, 4.2) 18: 5 ff ( 5.1, 5.2) 18: 6 ggg ( 6.1, 6.2) 18: 7 hhhh ( 7.1, 7.2) 18: 208 u (208.1, 208.2) 18: 9 jj ( 9.1, 9.2) 18: 10 kkk ( 10.1, 10.2) 18: 211 wwww (211.1, 211.2) 18: 212 x (212.1, 212.2) 18: 213 yy (213.1, 213.2) 18: 114 OOO (114.1, 114.2) 18: 115 PPPP (115.1, 115.2) 18: Example 38: Done running ./tiledb_array_read_dense_1 18: Example 39: Running ./tiledb_array_read_sparse_1... 18: coords a1 a2 (a3.first, a3.second) 18: -------------------------------------------------- 18: (1, 1) 0 a ( 0.1, 0.2) 18: (1, 2) 1 bb ( 1.1, 1.2) 18: (1, 4) 2 ccc ( 2.1, 2.2) 18: (2, 3) 3 dddd ( 3.1, 3.2) 18: (3, 1) 4 e ( 4.1, 4.2) 18: (3, 2) 104 u (104.1, 104.2) 18: (4, 1) 105 vvvv (105.1, 105.2) 18: (4, 2) 5 ff ( 5.1, 5.2) 18: (3, 3) 106 w (106.1, 106.2) 18: (3, 4) 107 yyy (107.1, 107.2) 18: Example 39: Done running ./tiledb_array_read_sparse_1 18: Example 40: Running ./tiledb_array_read_dense_2... 18: a1 18: ---- 18: Reading cells... 18: 9 18: 211 18: 212 18: Reading cells... 18: 213 18: 114 18: 115 18: Example 40: Done running ./tiledb_array_read_dense_2 18: Example 41: Running ./tiledb_array_read_sparse_2... 18: a1 18: ---- 18: Reading cells... 18: 104 18: 5 18: Reading cells... 18: 106 18: 107 18: Example 41: Done running ./tiledb_array_read_sparse_2 20/21 Test #18: ci_tests ......................... Passed 50.63 sec 21/21 Test #21: tools_tests ...................... Passed 121.62 sec 100% tests passed, 0 tests failed out of 21 Total Test time (real) = 122.04 sec make[1]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' 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/genomicsdb-1.4.4' # 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/genomicsdb-1.4.4 -Dclassworlds.conf=/etc/maven/m2-debian.conf -Dproperties.file.manual=/build/genomicsdb-1.4.4/debian/maven.properties org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/genomicsdb-1.4.4/debian -Dmaven.repo.local=/build/genomicsdb-1.4.4/debian/maven-repo --batch-mode -Ddebian.dir=/build/genomicsdb-1.4.4/debian -Ddebian.package=libgenomicsdb-java -Dmaven.repo.local=/build/genomicsdb-1.4.4/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... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.genomicsdb:genomicsdb:jar:1.4.4 [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 235, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] [INFO] ---------------------< org.genomicsdb:genomicsdb >---------------------- [INFO] Building org.genomicsdb:genomicsdb 1.4.4 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- debian-maven-plugin:2.6:install (default-cli) @ genomicsdb --- [INFO] Cleaning pom file: /build/genomicsdb-1.4.4/pom.xml.save with options: [INFO] --keep-pom-version --package=libgenomicsdb-java [INFO] --rules=/build/genomicsdb-1.4.4/debian/maven.rules [INFO] --ignore-rules=/build/genomicsdb-1.4.4/debian/maven.ignoreRules [INFO] --published-rules=/build/genomicsdb-1.4.4/debian/maven.publishedRules [INFO] Install jar for genomicsdb into /usr/share/java [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.910 s [INFO] Finished at: 2023-05-08T07:07:10+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibgenomicsdb-java --base-directory=/build/genomicsdb-1.4.4 --non-explore Analysing pom.xml... mh_unpatchpoms -plibgenomicsdb-java make[1]: Leaving directory '/build/genomicsdb-1.4.4' dh_auto_install -O--buildsystem=cmake -Nlibgenomicsdb-java cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/genomicsdb-1.4.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/genomicsdb-1.4.4 -B/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/vcfutils.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/vcf_sweep.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/vcf.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/thread_pool.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/tbx.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/synced_bcf_reader.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/sam.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/regidx.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/kstring.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/ksort.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/kseq.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/kroundup.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/knetfile.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/klist.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/khash_str2int.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/khash.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/kfunc.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/kbitset.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hts_os.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hts_log.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hts_endian.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hts_defs.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hts.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/hfile.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/faidx.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/cram.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/htslib/bgzf.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-tiledb.a -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-tiledb.so -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/tiledb/tiledb.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_constants.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_storage.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb/tiledb/tiledb_utils.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.a -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.1.4.4 -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.0 -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so.1.4.4" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/lib/x86_64-linux-gnu/libgenomicsdb.so -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/include/genomicsdb_exception.h -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/create_genomicsdb_workspace -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/create_genomicsdb_workspace" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/gt_mpi_gather -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/gt_mpi_gather" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf2genomicsdb_init -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf2genomicsdb_init" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf2genomicsdb -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf2genomicsdb" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcfdiff -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcfdiff" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf_histogram -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/vcf_histogram" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/consolidate_genomicsdb_array -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/consolidate_genomicsdb_array" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/test_genomicsdb_bcf_generator -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/test_genomicsdb_bcf_generator" to "/usr/lib/x86_64-linux-gnu/genomicsdb" -- Installing: /build/genomicsdb-1.4.4/debian/tmp/usr/bin/test_genomicsdb_importer -- Set runtime path of "/build/genomicsdb-1.4.4/debian/tmp/usr/bin/test_genomicsdb_importer" to "/usr/lib/x86_64-linux-gnu/genomicsdb" make[1]: Leaving directory '/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu' dh_install -O--buildsystem=cmake debian/rules execute_after_dh_install-arch make[1]: Entering directory '/build/genomicsdb-1.4.4' # 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/genomicsdb-1.4.4/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so /build/genomicsdb-1.4.4/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so: RUNPATH=/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/src/main:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-tiledb/core:/usr/lib/x86_64-linux-gnu/openmpi/lib:/build/genomicsdb-1.4.4/obj-x86_64-linux-gnu/genomicsdb-htslib /build/genomicsdb-1.4.4/debian/libgenomicsdb-jni/usr/lib/jni/libgenomicsdbjni.so: new RUNPATH: /usr/lib/x86_64-linux-gnu/genomicsdb make[1]: Leaving directory '/build/genomicsdb-1.4.4' jh_installjavadoc -O--buildsystem=cmake 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 jh_manifest -O--buildsystem=cmake 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/libgenomicsdb0/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so: DWARF compression not beneficial - old size 864759 new size 879934 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake 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: 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: 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: debian/libgenomicsdb0/usr/lib/x86_64-linux-gnu/genomicsdb/libgenomicsdb-hts.so contains an unresolvable reference to symbol lgamma: it's probably a plugin dpkg-shlibdeps: warning: 14 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libgenomicsdb-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libgenomicsdb-java: substitution variable ${maven:CompileDepends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'genomicsdb-tools-dbgsym' in '../genomicsdb-tools-dbgsym_1.4.4-3_amd64.deb'. dpkg-deb: building package 'genomicsdb-tools' in '../genomicsdb-tools_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-dev' in '../libgenomicsdb-dev_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb0' in '../libgenomicsdb0_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-jni' in '../libgenomicsdb-jni_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb-java' in '../libgenomicsdb-java_1.4.4-3_all.deb'. dpkg-deb: building package 'libgenomicsdb-jni-dbgsym' in '../libgenomicsdb-jni-dbgsym_1.4.4-3_amd64.deb'. dpkg-deb: building package 'libgenomicsdb0-dbgsym' in '../libgenomicsdb0-dbgsym_1.4.4-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../genomicsdb_1.4.4-3_amd64.buildinfo dpkg-genchanges --build=binary -O../genomicsdb_1.4.4-3_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2304883/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2304883/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/2304883 and its subdirectories I: Current time: Mon May 8 07:13:31 +14 2023 I: pbuilder-time-stamp: 1683479611